WO2023279093A1 - Compositions et méthodes permettant de favoriser la santé respiratoire - Google Patents

Compositions et méthodes permettant de favoriser la santé respiratoire Download PDF

Info

Publication number
WO2023279093A1
WO2023279093A1 PCT/US2022/073367 US2022073367W WO2023279093A1 WO 2023279093 A1 WO2023279093 A1 WO 2023279093A1 US 2022073367 W US2022073367 W US 2022073367W WO 2023279093 A1 WO2023279093 A1 WO 2023279093A1
Authority
WO
WIPO (PCT)
Prior art keywords
disclosed
bacterial
corynebacterium
strain
probiotics
Prior art date
Application number
PCT/US2022/073367
Other languages
English (en)
Inventor
Matthew Kelly
Patrick SEED
Original Assignee
Duke University
Ann And Robert H. Lurie Children's Hospital Of Chicago
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Duke University, Ann And Robert H. Lurie Children's Hospital Of Chicago filed Critical Duke University
Publication of WO2023279093A1 publication Critical patent/WO2023279093A1/fr

Links

Classifications

    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P11/00—Drugs for disorders of the respiratory system
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/66—Microorganisms or materials therefrom
    • A61K35/74—Bacteria
    • A61K35/741—Probiotics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/66—Microorganisms or materials therefrom
    • A61K35/74—Bacteria
    • A61K35/741—Probiotics
    • A61K35/744—Lactic acid bacteria, e.g. enterococci, pediococci, lactococci, streptococci or leuconostocs
    • A61K35/747—Lactobacilli, e.g. L. acidophilus or L. brevis
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P11/00—Drugs for disorders of the respiratory system
    • A61P11/02—Nasal agents, e.g. decongestants
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P11/00—Drugs for disorders of the respiratory system
    • A61P11/04—Drugs for disorders of the respiratory system for throat disorders
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P11/00—Drugs for disorders of the respiratory system
    • A61P11/14—Antitussive agents
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/689—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria

Definitions

  • Pneumonia is the leading infectious killer of children, accounting for more than 800,000 child deaths each year.
  • Streptococcus pneumoniae (pneumococcus) is a leading cause of severe infections among children and adults.
  • Streptococcus pneumoniae (Sp) causes most fatal cases of childhood pneumonia despite vaccination.
  • Colonization of the nasopharynx (NP) precedes infections by Sp, and the NP microbiota serves as a barrier to pathogen colonization. Interactions between commensal microbes in the upper respiratory tract and S. pneumoniae are poorly described.
  • FIG. 1A - FIG. IB show alpha diversity of the nasopharyngeal microbiome among mother-infant dyads in Botswana. Box plots depict nasopharyngeal microbiome diversity, as measured by the Shannon index (FIG. 1A), and richness, as measured by the number of unique ASVs (FIG. IB). Maternal nasopharyngeal samples are from the birth visit only (M0), and are shown in red, while nasopharyngeal samples from infants were sequenced at ten time points during the first year of life (10-112) and are shown in blue.
  • the Shannon index of the infant nasopharyngeal microbiome is higher at birth than at all later time points (Wilcoxon signed-rank tests, » ⁇ 0.0001) and compared to maternal samples (Wilcoxon signed-rank tests, /» ⁇ 0.0001).
  • the number of unique ASVs in infant nasopharyngeal samples is lower than in maternal samples from birth through five months of age (Wilcoxon signed-rank tests, » ⁇ 0.05).
  • FIG. 2A - FIG. 2B show the composition of the nasopharyngeal microbiome among mother-infant dyads in Botswana.
  • FIG. 2A shows the principal components (PCoA) plot based on Bray-Curtis distances showing nasopharyngeal microbiome composition among mothers at delivery (M0) and infants throughout the first year of life (10-112).
  • PCoA principal components
  • M0 mothers at delivery
  • nasopharyngeal microbiome composition progressively diverges from the composition of the adult nasopharyngeal microbiome.
  • Ellipses define the regions containing 80% of all samples that can be drawn from the underlying multivariate t distribution.
  • FIG. 3A - FIG. 3C shows state transitions of the nasopharyngeal microbiome during infancy.
  • Each nasopharyngeal sample was classified based on the dominant bacterial genus in that sample or, if no genus occupied > 50% of the sequencing reads, the sample was classified as biodiverse.
  • Each diagram depicts changes in infant nasopharyngeal microbiome biotype between two consecutive study visits.
  • FIG. 3A shows months 0 to 1, months 1 to 2, and months 2 to 3.
  • FIG. 3B shows months 3 to 4, months 4 to 5, and months 5 to 6.
  • FIG. 3C shows months 6 to 8, months 8 to 10, and months 10 to 12. Arrows point to the directionality of microbiome transitions while ribbon widths represent the frequency of these transitions.
  • the colors correspond to specific microbiome biotypes.
  • FIG. 4A - FIG. 4D show associations between environmental exposures and the composition of the nasopharyngeal microbiome during infancy.
  • MaAsLin2 was used to fit log- transformed generalized linear mixed models evaluating associations between sociodemographic factors and environmental exposures and the relative abundances of bacterial genera within the infant nasopharyngeal microbiome. The coefficients from these models, which correspond to the relative effect sizes of associations, are shown for significant associations (q ⁇ 0.20) identified for antibiotic exposures (FIG. 4A), the number of PCV-13 doses (FIG. 4B), breastfeeding (FIG. 4C), and the winter season (FIG. 4D).
  • FIG. 5A - FIG. 5C show strain-specific inhibition of pneumococcal growth by Corynebacterium. Two strains of S. pneumoniae , one reference strain (ATCC 6303; serotype 3) and one strain isolated from an infant nasopharyngeal sample (05-160; serotype 11 A) were separately added to sterile, cell-free media from overnight cultures of Corynebacterium strains. Growth of these strains of S.
  • FIG. 5A - FIG. 5C show growth curves of S. pneumoniae strains in different media, including cell-free media from inhibitory strains of C. accolens (05-122) (FIG. 5A), C. tuberculostearicum (05-144) (FIG. 5B), and C. coyleae (05-104) (FIG. 5C).
  • FIG. 5D - FIG. 5F show growth curves of S. pneumoniae strains in different media, including cell-free media from strains of C. accolens (05-161) (FIG. 5D), C. tuberculostearicum (05-150) (FIG.
  • TSB tryptic soy broth
  • BHIT-TSB brain heart infusion medium with 0.2% Tween80 diluted 50% with tryptic soy broth.
  • FIG. 6 shows the cumulative incidence curve for S. pneumoniae colonization among infants in Botswana. S. pneumoniae colonization was assessed through quantitative PCR testing of infant nasopharyngeal samples collected monthly (0-6 months) or bimonthly (6-12 months) during the first year of life.
  • FIG. 8 shows the adherence of C. accolens 05-122 (C122) and competition with Spa 05- 160 (SI 60) on A549 respiratory epithelium cells.
  • A549 monolayers at confluency were infected for 30 min at a multiplicity of infection (MOI) of 20:1 in a 96 well moderate throughput format using strains C122 or S160.
  • MOI multiplicity of infection
  • the left panel shows the percentage of adherent C122 and S160.
  • FIG. 9A - FIG. 9B shows Corynebacterium spp. species and strain-specific secretion of Sp growth inhibitors. Pneumococcal growth was determined by OD600 readings normalized to blank media controls.
  • FIG. 9A shows growth curves of S. pneumoniae strains in different media, including cell-free media from an inhibitory strain of C. tuberculostearicum (05-144).
  • FIG. 9B shows growth curves of S. pneumoniae strains in different media, including cell-free media from a strain of C. tuberculostearicum (05-150) that did not demonstrate pneumococcal growth inhibition. Similar inhibition was identified from C. coyleae , C. striatum , and C. accolens species with strain-dependent variation in inhibitory effects.
  • FIG. 10 shows the Corynebacterium pan-genome. 273 publicly available complete genomes for Corynebacterium spp. from NCBI were obtained. Anvio was used to create the display.
  • FIG. 11 shows adherence and invasion assays.
  • the left side shows the measurement of adherence of Corynebacterium strains to respiratory epithelium and right side shows assessment of inhibition of Sp adherence and invasion by Corynebacterium strains.
  • FIG. 12A - FIG. 12D shows the secretome assays.
  • FIG. 12A shows secretion of factors by Corynebacterium strains grown in liquid media.
  • FIG. 12B shows the assessment of Sp growth in the presence of supernatants from strain cultures.
  • FIG. 12C shows the secretion of factors by host respiratory epithelium in response to contact with Corynebacterium strains while
  • FIG. 12D shows assessment of Sp growth in the presence of supernatants from Corynebacterium-exposQd respiratory epithelium.
  • FIG. 13 shows power calculations. Power curves are shown for various sample and effect sizes using a pairwise model. All comparative analyses are anticipated to have at least 50 isolate pairs, indicating that >80% detects an effect size of 0.1.
  • Disclosed herein is a pharmaceutical formulation comprising a probiotic, and at least one pharmaceutically acceptable carrier.
  • a pharmaceutical formulation comprising a consortium of probiotics, and at least one pharmaceutically acceptable carrier.
  • a pharmaceutical formulation comprising factors secreted by a probiotic, and at least one pharmaceutically acceptable carrier.
  • a pharmaceutical formulation comprising factors secreted by a consortium of probiotics, and at least one pharmaceutically acceptable carrier.
  • a pharmaceutical formulation comprising at least one strain from the bacterial genus Corynebacterium.
  • a pharmaceutical formulation comprising one or more of at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus.
  • a method of promoting respiratory health in a subject comprising administering to a subject in need thereof a therapeutically effective amount of a biotherapeutic, wherein the biotherapeutic inhibits and/or prevents the growth of one or more pathogenic bacteria in one or more parts of the subject’s respiratory system.
  • a method of promoting respiratory health in a subject comprising administering to a subject in need thereof a therapeutically effective amount of a biotherapeutic, thereby inhibiting and/or preventing the growth of one or more pathogenic bacteria in one or more parts of the subject’s respiratory system.
  • Disclosed herein is a method of reducing the risk of developing a pathogenic bacterial infection, the method comprising administering to a subject in need thereof a therapeutically effective amount of a biotherapeutic, thereby preventing and/or inhibiting the colonization of the pathogenic bacteria.
  • a method of reducing the risk of developing a S. pneumoniae infection the method comprising administering to a subject in need thereof a therapeutically effective amount of a biotherapeutic, thereby preventing and/or inhibiting the colonization of S. pneumoniae.
  • Disclosed herein is a method of treating S.
  • a method of treating S. pneumoniae colonization in a subject comprising administering a therapeutically effective amount of a biotherapeutic to the subject in need thereof, wherein the colonization of S. pneumoniae in the subject’s respiratory system is inhibited and/or prevented following administration.
  • a method of treating S. pneumoniae colonization in a subject comprising administering a therapeutically effective amount of a biotherapeutic to the subject in need thereof, thereby inhibiting and/or preventing colonization of S. pneumoniae in the subject’s respiratory system.
  • Disclosed herein is a method of modulating microbial diversity or composition in a subject, the method comprising characterizing the microbiome of a biological sample obtained from a subject; and administering one or more biotherapeutics to the subject, wherein following administration, the microbiome is modulated.
  • kits comprising at least one strain from the bacterial genus Corynebacterium.
  • a kit comprising at least one strain from the bacterial genus Dolosigranulum.
  • a kit comprising at least one strain from the bacterial genus Streptococcus.
  • a kit comprising at least one strain from the bacterial genus Lactobacillus.
  • kits comprising at least one strain from the bacterial genus Corynebacterium sp., at least one strain from the bacterial genus Dolosigranulum sp., at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus.
  • a kit comprising a pharmaceutical formulation comprising at least one strain from the bacterial genus Corynebacterium.
  • a kit comprising a pharmaceutical formulation comprising at least one strain from the bacterial genus Dolosigranulum.
  • kits comprising a pharmaceutical formulation comprising at least one strain from the bacterial genus Streptococcus.
  • compositions compounds, kits, capsules, containers, and/or methods thereof. It is to be understood that the inventive aspects of which are not limited to specific synthetic methods unless otherwise specified, or to particular reagents unless otherwise specified, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular aspects only and is not intended to be limiting. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, example methods and materials are now described.
  • ASV amplicon sequence variant
  • ATCC American Type Culture Collection
  • BHI brain heart infusion
  • BHIT-TSB brain heart infusion medium with 0.2% Tween 80
  • Cl confidence interval
  • g gram
  • Hib Haemophilus influenzae type B
  • HR Hazard Ratio
  • IPD invasive pneumococcal disease
  • IQR interquartile range
  • MALDI-TOF MS matrix-assisted laser desorption ionization-time of flight mass spectrometry
  • OD600 optical density measured at a wavelength of 600 nanometer
  • PCR polymerase chain reaction
  • PCV-13 13-valent pneumococcal conjugate vaccine
  • RSV respiratory syncytial virus
  • rpm revolutions per minute
  • rRNA ribosomal RNA
  • TSB tryptic soy broth
  • Ranges can be expressed herein as from “about” one particular value, and/or to “about” another particular value. When such a range is expressed, a further aspect includes from the one particular value and/or to the other particular value. Similarly, when values are expressed as approximations, by use of the antecedent “about,” it will be understood that the particular value forms a further aspect. It will be further understood that the endpoints of each of the ranges are significant both in relation to the other endpoint and independently of the other endpoint. It is also understood that there are a number of values disclosed herein, and that each value is also herein disclosed as “about” that particular value in addition to the value itself. For example, if the value “10” is disclosed, then “about 10” is also disclosed. It is also understood that each unit between two particular units are also disclosed. For example, if 10 and 15 are disclosed, then 11, 12, 13, and 14 are also disclosed.
  • references in the specification and concluding claims to parts by weight of a particular element or component in a composition denotes the weight relationship between the element or component and any other elements or components in the composition or article for which a part by weight is expressed.
  • X and Y are present at a weight ratio of 2:5, and are present in such ratio regardless of whether additional components are contained in the compound.
  • a disclosed method can optionally comprise one or more additional steps, such as, for example, repeating an administering step or altering an administering step.
  • the term “subject” refers to the target of administration, e.g ., a human being.
  • the term “subject” also includes domesticated animals (e.g, cats, dogs, etc.), livestock (e.g, cattle, horses, pigs, sheep, goats, etc.), and laboratory animals (e.g, mouse, rabbit, rat, guinea pig, fruit fly, etc.).
  • the subject of the herein disclosed methods can be a vertebrate, such as a mammal, a fish, a bird, a reptile, or an amphibian.
  • the subject of the herein disclosed methods can be a human, non-human primate, horse, pig, rabbit, dog, sheep, goat, cow, cat, guinea pig, or rodent.
  • the term does not denote a particular age or sex, and thus, adult and child subj ects, as well as fetuses, whether male or female, are intended to be covered.
  • a subject can be a human patient.
  • a subject can have a respiratory infection, be suspected of having a respiratory infection, or be at risk of developing a respiratory infection.
  • diagnosisd means having been subjected to an examination by a person of skill, for example, a physician, and found to have a condition that can be diagnosed or treated by one or more of the disclosed biotherapeutics, the disclosed pharmaceutical formulations, or a combination thereof, or by one or more of the disclosed methods.
  • diagnosis with an infection means having been subjected to an examination by a person of skill, for example, a physician, and found to have a condition (such as, for example, a respiratory infection) that can be treated by one or more of the disclosed biotherapeutics, the disclosed pharmaceutical formulations, or any combination thereof, or by one or more of the disclosed methods.
  • “suspected of having an infection” can mean having been subjected to an examination by a person of skill, for example, a physician, and found to have a condition (such as a respiratory infection) that can likely be treated by one or more of by one or more of the disclosed biotherapeutics, the disclosed pharmaceutical formulations, or any combination thereof, or by one or more of the disclosed methods.
  • an examination can be physical, can involve various tests (e.g., blood tests, genotyping, biopsies, etc.), scans (e.g., CT scans, PET scans, etc.), and assays (e.g., enzymatic assay), or a combination thereof.
  • a “patient” refers to a subject at risk of or afflicted with an infection such as, for example, a respiratory infection.
  • a patient can refer to a subject that has been diagnosed with or is suspected of having a disease or disorder such as a respiratory infection.
  • a patient can refer to a subject that has been diagnosed with or is suspected of having a respiratory infection and is seeking treatment or receiving treatment for the respiratory infection).
  • a patient can be a healthy subject not having an infection and not at risk of developing an infection.
  • a probiotic refers to a microorganism such as a bacteria or yeast that is associated with positive effect for and/or confers an advantage to a subject.
  • a probiotic can comprise a single bacterial strain, a single bacterial strain (such as, for example, a strain of the bacterial species Corynebacterium accolens ), a consortium of bacterial strains from the same genus or species, or a consortium of bacterial strains of different genera or species (e.g., Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., and Lactobacillus sp.)
  • “Probiotic” as used herein refers to factors secreted from a microorganism such as a bacteria or yeast that are associated with positive effect for and/or confer an advantage to a subject.
  • a probiotic can comprise factors secreted from a single bacterial strain, a single bacterial species (such as, for example, Corynebacterium accolens ), a consortium of bacterial strains from the same genus or species, or a consortium of bacterial strains from different genera or species (e.g., Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., and Lactobacillus sp.)
  • a single bacterial species such as, for example, Corynebacterium accolens
  • a consortium of bacterial strains from the same genus or species e.g., Dolosigranulum sp ., Streptococcus sp ., and Lactobacillus sp.
  • postbiotics refers to functional bioactive compounds produced by probiotics and can be used to promote health.
  • the term postbiotics can be considered as a generic term for all synonyms and related terms for these microbial components. Therefore, postbiotics include metabolites, short chain fatty acids (SCFAs such as acetic acid, propionic acid, and butyric acid, etc.), microbial cell fractions, functional proteins, extracellular polysaccharides (EPS), cell lysates, acids, phenyl-lactic acid, volatile organic compounds (VOCs), B-vitamin synthesis (biotin, cobalamine, folic acid, nicotinic acid, pantothenic acid, pyridoxin, riboflavin, and thiamine), muropeptides derived from peptide glycans, antibacterial peptides (AMP) and pib types.
  • SCFAs short chain fatty acids
  • EPS extracellular polysaccharides
  • VOCs volatile organic compounds
  • the phrase “identified to be in need of treatment for a respiratory infection,” or the like refers to selection of a subj ect based upon need for treatment of the respiratory infection or a subject at risk of developing a respiratory infection.
  • a subject can be identified as having a need for treatment of a respiratory infection based upon an earlier diagnosis by a person of skill and thereafter subjected to treatment for the respiratory infection.
  • the identification can be performed by a person different from the person making the diagnosis.
  • the administration can be performed by one who performed the diagnosis.
  • inhibitor means to diminish or decrease an activity, level, response, condition, severity, disease, or other biological parameter.
  • This can include, but is not limited to, the complete ablation of the activity, growth, colonization, endocytosis, spread, expression level, response, condition, severity, disease, or other biological parameter.
  • This can also include, for example, a 10% inhibition or reduction in the activity, growth, colonization, endocytosis, spread, expression level, response, condition, severity, disease, or other biological parameter as compared to the native or control level (e.g., a subject not receiving one or more of the disclosed biotherapeutics, the disclosed pharmaceutical formulations, or a combination thereof).
  • the inhibition or reduction can be a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any amount of reduction in between as compared to native or control levels.
  • the inhibition or reduction can be 10-20%, 20- 30%, 30-40%, 40-50%, 50-60%, 60-70%, 70-80%, 80-90%, or 90-100% as compared to a native or control level (e.g., a subject not receiving one or more of the disclosed biotherapeutics, the disclosed pharmaceutical formulations, or a combination thereof).
  • the inhibition or reduction can be 0-25%, 25-50%, 50-75%, or 75-100% as compared to native or control levels.
  • a native or control level can be a pre-infection level (such as a pre-respiratory infection state).
  • treat or “treating” or “treatment” include palliative treatment, that is, treatment designed for the relief of symptoms rather than the curing of the infection, disease, pathological condition, or disorder; preventative treatment, that is, treatment directed to minimizing or partially or completely inhibiting the development of the associated infection, disease, pathological condition, or disorder; and supportive treatment, that is, treatment employed to supplement another specific therapy directed toward the improvement of the associated infection, disease, pathological condition, or disorder.
  • the terms cover any treatment of a subject, including a mammal (e.g., a human), and includes: (i) preventing the undesired infection, physiological change, disease, pathological condition, or disorder from occurring in a subject that can be predisposed to the disease but has not yet been diagnosed as having it; (ii) inhibiting the infection, physiological change, disease, pathological condition, or disorder, i.e., arresting its development; or (iii) relieving the infection, physiological change, disease, pathological condition, or disorder, i.e ., causing regression of the disease.
  • a mammal e.g., a human
  • treating an infection can reduce the severity of an established infection in a subject by 1%- 100% as compared to a control (such as, for example, an individual not having a respiratory infection).
  • treating can refer to a 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% reduction in the severity of the infection (e.g., a respiratory infection).
  • treating an infection can reduce one or more symptoms of a disease or disorder in a subject by 1%-100% as compared to a control (such as, for example, an individual not having an infection such as a respiratory infection).
  • treating can refer to 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100% reduction of one or more symptoms of an established infection. It is understood that treatment does not necessarily refer to a cure or complete ablation or eradication of an infection. However, in an aspect, treatment can refer to a cure or complete ablation or eradication of an infection (such as a respiratory infection).
  • the term “prevent” or “preventing” or “prevention” refers to precluding, averting, obviating, forestalling, stopping, or hindering something from happening, especially by advance action. It is understood that where reduce, inhibit, or prevent are used herein, unless specifically indicated otherwise, the use of the other two words is also expressly disclosed. In an aspect, preventing a respiratory infection is intended.
  • the words “prevent”, “preventing”, and “prevention” also refer to prophylactic or preventative measures for protecting or precluding a subject (e.g., an individual) not having an infection (such as a respiratory infection) or related complication from progressing to that complication. In an aspect, preventing a respiratory infection is intended.
  • administering refers to any method of providing to a subject one or more of the disclosed biotherapeutics, the disclosed pharmaceutical formulations, or any combination thereof.
  • Such methods are well known to those skilled in the art and include, but are not limited to, the following: oral administration, transdermal administration, administration by inhalation, nasal administration or administration into other sites in the upper respiratory tract, topical administration, in utero administration, intratumoral administration, intrahepatic administration, intravaginal administration, ophthalmic administration, intraaural administration, otic administration, intracerebral administration, rectal administration, sublingual administration, buccal administration, and parenteral administration, including injectable such as intravenous administration, intra-CSF administration, intra-arterial administration, intramuscular administration, and subcutaneous administration.
  • Administration can be continuous or intermittent.
  • Administration can comprise a combination of one or more routes.
  • the skilled person can determine an efficacious dose, an efficacious schedule, and an efficacious route of administration of one or more of the disclosed biotherapeutics, the disclosed pharmaceutical formulations, or any combination thereof to treat or prevent an infection (such as a respiratory infection).
  • the skilled person can also alter, change, or modify an aspect of an administering step to improve efficacy of the disclosed biotherapeutics, the disclosed pharmaceutical formulations, or any combination thereof.
  • determining the amount is meant both an absolute quantification of a particular analyte (e.g., biomarker for an infection) or a determination of the relative abundance of a particular pathogenic and/or non-pathogenic bacteria (e.g., Corynebacterium sp. or S. pneumoniae).
  • the phrase includes both direct or indirect measurements of abundance or both.
  • the proportional abundance for each nasal bacterial taxon can be determined by (Number of sequences assigned to the taxon from the sample) / (Total number of sequences from the sample), which can be combined with nasal bacterial density to calculate taxon absolute abundance as (Proportional abundance of the taxon from the sample) x (Nasal bacterial density of the sample).
  • the cultivation of specific organisms per total sample collection can also an acceptable method for calculating abundance.
  • modifying the method can comprise modifying or changing one or more features or aspects of one or more steps of a disclosed method.
  • a method can be altered by changing the amount of the disclosed biotherapeutic, the disclosed pharmaceutical formulation, or disclosed therapeutic agent administered to a subj ect, or by changing the frequency of administration of the disclosed biotherapeutic, the disclosed pharmaceutical formulation, or the disclosed therapeutic agent, by changing the duration of time that the disclosed biotherapeutic, the disclosed pharmaceutical formulation, or the disclosed therapeutic agent, or by substituting for one or more of the disclosed components and/or reagents with a similar or equivalent component and/or reagent.
  • a pharmaceutical carrier refers to sterile aqueous or nonaqueous solutions, dispersions, suspensions or emulsions, as well as sterile powders for reconstitution into sterile injectable solutions or dispersions just prior to use.
  • suitable aqueous and nonaqueous carriers, diluents, solvents, or vehicles include water, ethanol, polyols (such as glycerol, propylene glycol, polyethylene glycol and the like), carboxymethylcellulose and suitable mixtures thereof, vegetable oils (such as olive oil) and injectable organic esters such as ethyl oleate.
  • a pharmaceutical carrier employed can be a solid, liquid, or gas.
  • examples of solid carriers can include lactose, terra alba, sucrose, talc, gelatin, agar, pectin, acacia, magnesium stearate, and stearic acid.
  • examples of liquid carriers can include sugar syrup, peanut oil, olive oil, and water.
  • examples of gaseous carriers can include carbon dioxide and nitrogen.
  • oral liquid preparations such as suspensions, elixirs and solutions
  • carriers such as starches, sugars, microcrystalline cellulose, diluents, granulating agents, lubricants, binders, disintegrating agents, and the like
  • oral solid preparations such as powders, capsules and tablets.
  • tablets and capsules are the preferred oral dosage units whereby solid pharmaceutical carriers are employed.
  • tablets can be coated by standard aqueous or nonaqueous techniques.
  • Proper fluidity can be maintained, for example, by the use of coating materials such as lecithin, by the maintenance of the required particle size in the case of dispersions and by the use of surfactants.
  • These compositions can also contain adjuvants such as preservatives, wetting agents, emulsifying agents and dispersing agents.
  • Prevention of the action of microorganisms can be ensured by the inclusion of various antibacterial and antifungal agents such as paraben, chlorobutanol, phenol, sorbic acid and the like. It can also be desirable to include isotonic agents such as sugars, sodium chloride and the like.
  • Prolonged absorption of the injectable pharmaceutical form can be brought about by the inclusion of agents, such as aluminum monostearate and gelatin, which delay absorption.
  • Injectable depot forms are made by forming microencapsule matrices of the drug in biodegradable polymers such as polylactide-polyglycolide, poly(orthoesters) and poly(anhydrides). Depending upon the ratio of drug to polymer and the nature of the particular polymer employed, the rate of drug release can be controlled. Depot injectable formulations are also prepared by entrapping the drug in liposomes or microemulsions that are compatible with body tissues.
  • the injectable formulations can be sterilized, for example, by filtration through a bacterial-retaining filter or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved or dispersed in sterile water or other sterile injectable media just prior to use.
  • Suitable inert carriers can include sugars such as lactose. Desirably, at least 95% by weight of the particles of the active ingredient have an effective particle size in the range of 0.01 to 10 micrometers.
  • the term “excipient” refers to an inert substance which is commonly used as a diluent, vehicle, preservative, binder, or stabilizing agent, and includes, but is not limited to, proteins (e.g., serum albumin, etc.), amino acids (e.g., aspartic acid, glutamic acid, lysine, arginine, glycine, histidine, etc.), fatty acids and phospholipids (e.g., alkyl sulfonates, caprylate, etc.), surfactants (e.g., SDS, polysorbate, nonionic surfactant, etc.), saccharides (e.g., sucrose, maltose, trehalose, etc.) and polyols (e.g., mannitol, sorbitol, etc.). See, also, for reference, Remington’s Pharmaceutical Sciences, (1990) Mack Publishing Co., Easton, Pa., which is hereby
  • “concurrently” means (1) simultaneously in time, or (2) at different times during the course of a common treatment schedule.
  • contacting refers to bringing one or more of the disclosed biotherapeutics, the disclosed pharmaceutical formulations, or any combination thereof together with a target area or intended target area (e.g., such as an aspect of the respiratory system affected by an infection) in such a manner that the disclosed biotherapeutic, the disclosed pharmaceutical formulation, or any combination thereof can exert an effect on the intended target or targeted area either directly or indirectly.
  • a target area or intended target area e.g., such as an aspect of the respiratory system affected by an infection
  • a target area or intended target area can be one or more parts of a subject’s respiratory system (e.g., the subject’s mouth, nose, ears, sinuses, nasopharynx or oropharynx, trachea, bronchial tubes, lungs, alveoli, bronchioles, capillaries, lung lobes, pleura, cilia, epiglottis, larynx, or any combination thereof).
  • a target area or intended target area can be any cell or any organ infected by pathogenic bacteria and/or S. pneumoniae.
  • a target area or intended target area can be any organ, tissue, or cells that are affected by an infection.
  • determining can refer to measuring or ascertaining the presence and severity of an infection, such as a respiratory infection.
  • Methods and techniques used to determine the presence and/or severity of an infection are typically known to the medical arts.
  • the art is familiar with the ways to identify and/or diagnose the presence, severity, or both of an infection (such as, for example, a respiratory infection).
  • an effective amount and “amount effective” can refer to an amount that is sufficient to achieve the desired result such as, for example, the treatment and/or prevention of an infection (e.g., a respiratory infection) or a suspected infection.
  • the terms “effective amount” and “amount effective” can refer to an amount that is sufficient to achieve the desired an effect on an undesired condition (e.g., a respiratory infection).
  • a “therapeutically effective amount” refers to an amount that is sufficient to achieve the desired therapeutic result or to have an effect on undesired symptoms, but is generally insufficient to cause adverse side effects.
  • “therapeutically effective amount” means an amount of a disclosed biotherapeutic, a disclosed pharmaceutical formulation, or any combination thereof that (i) treats the particular infection, disease, condition, or disorder (e.g., a respiratory infection), (ii) attenuates, ameliorates, or eliminates one or more symptoms of the particular infection, disease, condition, or disorder (e.g., a respiratory infection), or (iii) delays the onset of one or more symptoms of the particular infection, disease, condition, or disorder described herein (e.g., a respiratory infection).
  • a respiratory infection e.g., a respiratory infection
  • attenuates, ameliorates, or eliminates one or more symptoms of the particular infection, disease, condition, or disorder e.g., a respiratory infection
  • delays the onset of one or more symptoms of the particular infection, disease, condition, or disorder described herein e.g., a respiratory infection.
  • the specific therapeutically effective dose level for any particular patient can depend upon a variety of factors including the disorder being treated and the severity of the infection; the disclosed biotherapeutics, the disclosed pharmaceutical formulations, or any combination thereof employed in the disclosed methods; the age, body weight, general health, sex and diet of the patient; the time of administration; the route of administration; the rate of excretion of the disclosed biotherapeutics, the disclosed pharmaceutical formulations, or any combination thereof employed; the duration of the treatment; other drugs used in combination or coincidental with the disclosed biotherapeutics, the disclosed pharmaceutical formulations, or any combination thereof, and other like factors well known in the medical arts.
  • the effective daily dose can be divided into multiple doses for purposes of administration. Consequently, a single dose of the disclosed biotherapeutics, the disclosed pharmaceutical formulations, or any combination thereof can contain such amounts or submultiples thereof to make up the daily dose.
  • the dosage can be adjusted by the individual physician in the event of any contraindications. Dosage can vary, and can be administered in one or more dose administrations daily, for one or several days. Guidance can be found in the literature for appropriate dosages for given classes of pharmaceutical products.
  • a preparation can be administered in a “prophylactically effective amount”; that is, an amount effective for prevention of an infection.
  • sequence identity and “sequence similarity” can be determined by alignment of two peptide or two nucleotide sequences using global or local alignment algorithms. Sequences may then be referred to as “substantially identical” or “essentially similar” when they are optimally aligned. For example, sequence similarity or identity can be determined by searching against databases such as FASTA, BLAST, etc., but hits should be retrieved and aligned pairwise to compare sequence identity.
  • Two proteins or two protein domains, or two nucleic acid sequences can have “substantial sequence identity” if the percentage sequence identity is at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more, preferably 90%, 95%, 98%, 99% or more.
  • Such sequences are also referred to as “variants” herein, e.g., other variants of a missing, deficient, and/or mutant protein or enzyme. It should be understood that sequence with substantial sequence identity do not necessarily have the same length and may differ in length. For example, sequences that have the same nucleotide sequence but of which one has additional nucleotides on the 3’- and/or 5’-side are 100% identical.
  • package insert is used to refer to instructions customarily included in commercial packages of therapeutic products, that contain information about the indications, usage, dosage, administration, contraindications and/or warnings concerning the use of such therapeutic products.
  • the term “in combination” in the context of the administration of other therapies includes the use of more than one therapy (e.g., drug therapy).
  • Administration “in combination with” one or more further therapeutic agents includes simultaneous (e.g., concurrent) and consecutive administration in any order.
  • the use of the term “in combination” does not restrict the order in which therapies are administered to a subject.
  • a first therapy e.g., a disclosed biotherapeutic or a disclosed pharmaceutical formulation
  • a second therapy e.g., a disclosed biotherapeutic or a disclosed pharmaceutical formulation
  • a second therapy e.g., a disclosed biotherapeutic or a
  • a pharmaceutical formulation comprising one or more disclosed biotherapeutics, disclosed secreted factors, disclosed consortia of probiotics, disclosed probiotics, or any combination thereof, and at least one pharmaceutically acceptable carrier.
  • a pharmaceutical formulation comprising biotherapeutic, and at least one pharmaceutically acceptable carrier.
  • a disclosed biotherapeutic can comprise a probiotic or a consortium of probiotics.
  • a pharmaceutical formulation comprising a probiotic, and at least one pharmaceutically acceptable carrier.
  • a pharmaceutical formulation comprising a consortium of probiotics, and at least one pharmaceutically acceptable carrier.
  • a pharmaceutical formulation comprising factors secreted by a probiotic, and at least one pharmaceutically acceptable carrier.
  • a pharmaceutical formulation comprising factors secreted by a consortium of probiotics, and at least one pharmaceutically acceptable carrier.
  • a disclosed pharmaceutical formulation can further comprise a growth medium to sustain a disclosed probiotic or a disclosed consortium of probiotics prior to administration to the subject.
  • a disclosed probiotic in an aspect of a disclosed pharmaceutical formulation, can be lyophilized or freeze-dried. In an aspect of a disclosed pharmaceutical formulation, a disclosed consortium of probiotics can be lyophilized or freeze-dried.
  • a disclosed pharmaceutical formulation can comprise at least one lyoprotectant.
  • a disclosed lyoprotectant can comprise peptone, glycerol, lactose, gelatin, glucose, sucrose, trehalose, dextran, maltodextrin, adonitol, sodium glutamate, or any combination thereof. Lyoprotectants are known to those skilled in the art.
  • a disclosed pharmaceutical formulation can comprise at least one gelling agent, preferably a pharmaceutically acceptable gelling agent.
  • a disclosed pharmaceutical formulation can comprise at least preservative such as, for example, benzyl alcohol, cresols, benzoic acid, phenol, parabens, or sorbic acid.
  • a disclosed pharmaceutical formulation can comprise at least one stabilizer such as, for example, a surfactant, a polymer, a polyol, a poloxamer, an albumin, a gelatin, a trehalose, a protein, a sugar, a polyvinylpyrrolidone, a N-acetyl-tryptophan (NAT), a caprylate (e.g., sodium caprylate), a polysorbate (e.g., P80), an amino acid, and a divalent metal cation (e.g., zinc).
  • stabilizer such as, for example, a surfactant, a polymer, a polyol, a poloxamer, an albumin, a gelatin, a trehalose, a protein, a sugar, a polyvinylpyrrolidone, a N-acetyl-tryptophan (NAT), a caprylate (e.g., sodium caprylate), a polysorbate (e
  • a disclosed biotherapeutic can comprise one or more probiotics.
  • a disclosed consortium of probiotics can comprise at least one strain from the bacterial genus Corynebacterium, at least one strain from the bacterial genus Dolosigranulum , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus.
  • the at least one strain from the bacterial genus Cory neb acterium can comprise one or more strains of Corynebacterium accolens.
  • the at least one strain from the bacterial genus Dolosigranulum can comprise one or more strains of Dolosigranulum pigrum.
  • the at least one strain from the bacterial genus Streptococcus can comprise one or more strains of Streptococcus mitis, Streptococcus salivarius , Streptococcus oralis , or Streptococcus thermophilus .
  • the at least one strain from the bacterial genus Lactobacillus can comprise one or more strains of Lactobacillus rhamnosus or Lactobacillus acidophilus.
  • one or more disclosed probiotics can comprise at least one strain from the bacterial genus one Corynebacterium sp. In an aspect of a disclosed pharmaceutical formulation, one or more disclosed probiotics can comprise at least one strain from the bacterial genus Corynebacterium and at least one strain from the bacterial genus Dolosigranulum. In an aspect of a disclosed pharmaceutical formulation, one or more disclosed probiotics can comprise at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , and at least one strain from the bacterial genus Streptococcus.
  • one or more disclosed probiotics can comprise at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , and at least one strain from the bacterial genus Lactobacillus. In an aspect of a disclosed pharmaceutical formulation, one or more disclosed probiotics can comprise at least one strain from the bacterial genus Corynebacterium and at least one at least one strain from the bacterial genus Streptococcus.
  • one or more disclosed probiotics can comprise at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus. In an aspect of a disclosed pharmaceutical formulation, one or more probiotics can comprise at least one strain from the bacterial genus Corynebacterium and at least one strain from the bacterial genus Lactobacillus.
  • one or more probiotics can comprise at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus.
  • a disclosed biotherapeutic can comprise one or more factors secreted by a disclosed probiotic or secreted by a disclosed consortium of probiotics.
  • a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus.
  • a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium. In an aspect of a disclosed pharmaceutical formulation, a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium and at least one strain from the bacterial genus Dolosigranulum. In an aspect of a disclosed pharmaceutical formulation, a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , and at least one train from the bacterial genus Streptococcus.
  • a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , and at least one strain from the bacterial genus Lactobacillus.
  • a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium and at least one strain from the bacterial genus Streptococcus.
  • a disclosed biotherapeutic can comprise comprises one or more factors secreted by at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus.
  • a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium and at least one strain from the bacterial genus Lactobacillus.
  • a disclosed strain from the bacterial genus Corynebacterium can comprise C. accolens , C.
  • afermentans subsp. afermentans C. afermentans subsp. lipophilum , C. ammoniagenes , C. amycolatum , C. appendicis , C. aquaticum , C. arge ntorate use, C. city pi cum, C. aurimucosum , C. auris, C. bovis, C. canis, C. confusum , C. coyleae , C. diphtheriae , C. durum , C. efficiens , C. equi (now Rhodococcus equi ), C. falsenii , C. flavescens , C. grisburgense , C.
  • C. parvum Propionibacterium acnes
  • C. paurometabolum C. pilbarense
  • C. propinquum C. pseudodiphtheriticum (C. hofinannii )
  • C. pseudotuberculosis C. pyogenes-Trueperella pyogenes
  • C. pyruviciproducens C. renale, C. resistans, C. riegelii, C. simulans, C. singular, C. spec, C. sputi, C. stationis, C. striatum, C. sundsvallense, C. tenuis, C. thomsenii, C. timonense, C.
  • tuberculostearicum C. tuscaniense, C. ulcerans, C. urealyticum (group D2), C. urealyticum, C. xerosis, Corynebacterium BWA136, Corynebacterium BWA297 , Corynebacterium DU041, Corynebacterium DU044 , or any combination thereof.
  • a disclosed strain from the bacterial genus Corynebacterium can comprise C. accolens, C. coyleae, C. propinquum, C. pseudodiphtheriticum, C. amycolatum, C. glutamicum, C. aurimucosum, C. tuberculostearicum, C. afermentans, C. striatum, Corynebacterium DU041, Corynebacterium DU044, Corynebacterium BWA136, Corynebacterium BWA297 , or any combination thereof.
  • a disclosed strain from the bacterial genus Corynebacterium can comprise any species identified in Table 13.
  • a disclosed therapeutically effective dose can comprise a total of at least 100 bacterial CFUs of the one or more probiotics, a total of at least 200 to at least 300 bacterial CFUs of the one or more probiotics, a total of at least 300 to at least 400 bacterial CFUs of the one or more probiotics, a total of at least 400 to at least 500 bacterial CFUs of the one or more probiotics, a total of at least 500 to at least 600 bacterial CFUs of the one or more probiotics, a total of at least 600 to at least 700 bacterial CFUs of the one or more probiotics, a total of at least 700 to at least 800 bacterial CFUs of the one or more probiotics, a total of at least 800 to at least 900 bacterial CFUs of the one or more probiotics, a total of at least 900 to at least 1000 bacterial CFUs of the one or more probiotics, or a total of at least 1000 bacterial CFUs of the one or more probiotics,
  • a disclosed therapeutically effective dose can comprise a total of at least 1000 to at least 2000 bacterial CFUs of the one or more probiotics, a total of at least 2000 to at least 3000 bacterial CFUs of the one or more probiotics, a total of at least 3000 to at least 4000 bacterial CFUs of the one or more probiotics, a total of at least 4000 to at least 5000 bacterial CFUs of the one or more probiotics, a total of at least 5000 to at least 6000 bacterial CFUs of the one or more probiotics, a total of at least 6000 to at least 7000 bacterial CFUs of the one or more probiotics, a total of at least 8000 to at least 9000 bacterial CFUs of the one or more probiotics, or a total of at least 10,000 bacterial CFUs of one or more disclosed probiotics (such as, for example, at least one strain from the bacterial genus Corynebacterium,
  • a disclosed therapeutically effective dose can comprise a total of at least 100 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 200 to at least 300 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 300 to at least 400 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp.
  • Lactobacillus sp ., or any combination thereof a total of at least 400 to at least 500 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 500 to at least 600 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 600 to at least 700 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 700 to at least 800 bacterial CFUs of Corynebacterium sp ., Dolosi
  • Lactobacillus sp ., or any combination thereof a total of at least 800 to at least 900 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 900 to at least 1000 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, or a total of at least 1000 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof.
  • a disclosed therapeutically effective dose can comprise a total of at least 1000 to at least 2000 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 2000 to at least 3000 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 3000 to at least 4000 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp., Streptococcus sp.
  • Lactobacillus sp ., or any combination thereof a total of at least 4000 to at least 5000 bacterial CFUs of the Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 5000 to at least 6000 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 6000 to at least 7000 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 8000 to at least 9000 bacterial CFUs of Corynebacterium
  • a disclosed therapeutically effective dose can comprise a total of at least 10 4 to at least 10 5 bacterial CFUs of the one or more probiotics, a total of at least 10 5 to at least 10 6 bacterial CFUs of the one or more probiotics, a total of at least 10 6 to at least 10 7 bacterial CFUs of the one or more probiotics, a total of at least 10 7 to at least 10 8 bacterial CFUs of the one or more probiotics, a total of at least 10 8 to at least 10 9 bacterial CFUs of the one or more probiotics, a total of at least 10 9 to at least 10 10 bacterial CFUs of the one or more probiotics, a total of at least 10 10 to at least 10 11 bacterial CFUs of the one or more probiotics, a total of at least 10 11 to at least 10 12 bacterial CFUs of the one or more probiotics, a total of at least 10 12 bacterial CFUs of the one or more probiotics,
  • a disclosed therapeutically effective dose can comprise at least 10 3 , 10 4 , 10 5 , 10 6 , 10 7 , 10 8 , 10 9 , 10 10 , 10 11 , or 10 12 CFUs of a disclosed probiotic or a consortium of disclosed probiotics, preferably at least 1.2 x 10 3 , 1.4 x 10 3 ,
  • 2 x 10 3 or 3 x 10 3 CFUs of a disclosed probiotic or a consortium of disclosed probiotics, at least 5 x 10 3 , 5.02 x 10 3 , 5.04 x 10 3 , 5.2 x 10 3 , or 5.4 x 10 3 CFUs of a disclosed probiotic or a consortium of disclosed probiotics, at least 1.02 x 10 4 , 1.04 x 10 4 , 1.2 x 10 4 , 1.4 x 10 4 , 1.5 x 10 4 , 2 x 10 4 , or
  • 3 x 10 4 CFUs of a disclosed probiotic or a consortium of disclosed probiotics at least 5 x 10 4 , 5.02 x 10 4 , 5.04 x 10 4 , 5.2 x 10 4 , or 5.4 x 10 4 CFUs of a disclosed probiotic or a consortium of disclosed probiotics, at least 1.02 x 10 5 , 1.04 x 10 5 , 1.2 x 10 5 , 1.4 x 10 5 , 1.5 x 10 5 , 2 x 10 5 , or 3 x 10 5 CFUs of a disclosed probiotic or a consortium of disclosed probiotics, at least 1.02 x 10 6 , 1.04 x 10 6 , 1.2 x 10 6 , 1.4 x 10 6 , 2 x 10 6 , or 3 x 10 6 CFUs of a disclosed probiotic or a consortium of disclosed probiotics, at least 1.02 x 10 7 , 1.04 x 10 7 , 1.2 x 10 7 , 1.4 x 10 7
  • a disclosed therapeutically effective dose can comprise any amount or an unlimited amount of bacterial CFUs of the one or more probiotics.
  • a disclosed therapeutically effective dose can comprise Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., and Lactobacillus sp. in a ratio of about 1 :0.01 :0.01 :0.01 to about 1 : 1 : 1 : 1.
  • a disclosed therapeutically effective dose can comprise Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., and Lactobacillus sp. in any ratio.
  • a disclosed therapeutically effective dose can comprise a higher dose of Corynebacterium sp ., or a higher dose of Dolosigranulum sp ., or a higher dose of Streptococcus sp ., or a higher dose of Lactobacillus sp. as compared to any other bacteria in the consortium.
  • a disclosed therapeutically effective dose can comprise a dose of Lactobacillus sp. that is about double that of Corynebacterium sp.
  • a disclosed pharmaceutical formulation can be prepared for systemic or direct administration.
  • a disclosed pharmaceutical formulation can be prepared for oral administration, intravenous administration, intranasal administration, sublingual administration, intraperitoneal administration, or any combination thereof.
  • a disclosed pharmaceutical formulation can be prepared for any method of administration disclosed herein.
  • a disclosed pharmaceutical formulation can be prepared for administration via multiple routes either concurrently or sequentially.
  • a disclosed pharmaceutical formulation can further comprise (i) one or more active agents, (ii) one or more biologically active agents, (iii) one or more pharmaceutically active agents, (iv) one or more immune-based therapeutic agents, (v) one or more clinically approved agents, or (vi) any combination thereof.
  • a disclosed pharmaceutical formulation can comprise one or more anti -bacterial agents.
  • the dose of an active agent, a biologically active agent, a pharmaceutically active agent, an immune-based therapeutic active agent, a clinically approved agent, or an anti -bacterial agent can be about 1 ng/kg body weight/day to about 100 ng/kg body weight/day, about 10 ng/kg body weight/day to about 1 pg/kg body, about 100 ng/kg body weight/day to about 10 pg/kg body, about 1 pg/kg body weight/day to about 100 pg/kg body, about 10 pg/kg body weight/day to about 1 mg/kg body, or about 100 pg/kg body weight/day to about 10 mg/kg body.
  • a disclosed pharmaceutical formulation can be administered to a healthy subject, for example, a subject that does not have an infection and/or is not suspected of having an infection.
  • a disclosed pharmaceutical formulation can promote a subject’s respiratory health, can inhibit and/or prevent the growth and/or spread of pathogenic bacteria and/or S. pneumoniae , can inhibit and/or prevent the adherence and/or colonization of pathogenic bacteria and/or S. pneumoniae , can modulate the endocytosis or paracellular migration of pathogenic bacteria and/or S. pneumoniae , can inhibit and/or prevent the spread of pathogenic bacteria and/or S. pneumoniae by competitive adherence and/or niche occupancy, or any combination thereof.
  • a repository of microbiome sequence data generated by one or more methods disclosed here.
  • a repository of microbiome sequence data available at Accession No. PRJNA698366 in the Sequence Read Archive (available at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA698366/).
  • a disclosed repository of microbiome sequence data can comprise data generated from about 1622 biosamples or SRA experiments.
  • a method of promoting respiratory health in a subject comprising administering to a subject in need thereof a therapeutically effective amount of a biotherapeutic, wherein the biotherapeutic inhibits and/or prevents the growth of one or more pathogenic bacteria in one or more parts of the subject’s respiratory system.
  • a method of promoting respiratory health in a subject comprising administering to a subject in need thereof a therapeutically effective amount of a biotherapeutic, thereby inhibiting and/or preventing the growth of one or more pathogenic bacteria in one or more parts of the subject’s respiratory system.
  • a subject can be any subject.
  • a subject that does not have an infection and/or is not suspected of having an infection.
  • a disclosed method can further comprise characterizing the microbiome of a biological sample.
  • a disclosed microbiome can comprise the nasopharyngeal microbiome, the nasal microbiome, or both.
  • a disclosed method can further comprise obtaining a biological sample from the subject.
  • a disclosed biological sample can comprise a nasal swab or lavage, a nasopharyngeal swab or lavage, or a pharyngeal swab or lavage, or any combination thereof.
  • a disclosed biological sample can comprise nasal secretion and/or cough droplets.
  • characterizing the microbiome can comprise (i) collecting a biological sample from the subject; (ii) extracting nucleic acid from the subject’s biological sample; and (iii) sequencing the extracted nucleic acid.
  • sequencing the extracted nucleic acid can generate sequence data.
  • characterizing the microbiome can further comprise analyzing the sequence data using taxonomic classification.
  • using taxonomic classification can comprise PCR amplification.
  • PCR amplification can comprise using primers targeting the 16S rRNA gene.
  • PCR amplification can comprise primers targeting the V4 variable region of the 16S rRNA gene.
  • disclosed primers can comprise a pair of primers.
  • a disclosed pair of primers can comprise a primer having the sequence of SEQ ID NO:01 and a primer having the sequence of SEQ ID NO:02.
  • a disclosed pair of primers can comprise a primer having the sequence of SEQ ID NO:03 and a primer having the sequence of SEQ ID NO:04. In an aspect, a disclosed pair of primers can comprise a primer having the sequence of SEQ ID NO:05 and a primer having the sequence of SEQ ID NO:06.
  • a disclosed method of promoting respiratory health can further comprise identifying the one or more pathogenic bacteria.
  • the disclosed pathogenic bacteria can comprise Streptococcus sp.
  • Streptococcus sp. can comprise S. pneumoniae.
  • the disclosed pathogenic bacteria can comprise Staphylococcus sp.
  • Staphylococcus sp. can comprise methicillin-sensitive S. aureus or methicillin-resistant S. aureus.
  • the disclosed pathogenic bacteria can comprise Haemophilus influenzae or Moraxella catarrhalis.
  • a disclosed method of promoting respiratory health can further comprise diagnosing the subject with an infection.
  • a diagnosed infection can comprise a respiratory infection.
  • a diagnosed infection can affect the subject’s mouth, nose, ears, sinuses, pharynx, trachea, bronchial tubes, lungs, alveoli, bronchioles, capillaries, lung lobes, pleura, cilia, epiglottis, larynx, or any combination thereof.
  • a disclosed method of promoting respiratory health can further comprise diagnosing the subject with pneumonia, otitis media, sinusitis, rhinosinusitis, or any combination thereof.
  • otitis media can be considered a general term for middle-ear inflammation and can be classified clinically as acute otitis media (AOM), recurrent AOM, OM with effusion (OME), or chronic OME, chronic suppurative OM (CSOM), or middle ear effusion (MEE).
  • AOM acute otitis media
  • OME recurrent AOM
  • OME OM with effusion
  • CSOM chronic suppurative OM
  • MEE middle ear effusion
  • sinusitis can occur when the tissue lining of the sinuses becomes swollen or inflamed.
  • Sinusitis can comprise acute sinusitis (e.g., when symptoms are present for 4 weeks or less), chronic sinusitis (e.g., when the swelling of the sinuses is present for longer than 3 months), or subacute sinusitis (e.g., when the swelling is present between one and three months).
  • rhinosinusitis can occur when the mucosal lining in the paranasal sinuses and nasal cavity becomes inflamed. Most cases of acute rhinosinusitis are caused by viral upper respiratory infections.
  • a disclosed biotherapeutic can comprise a probiotic, a consortium of probiotics, factors secreted from a probiotic, factors secreted from a consortium of probiotics, or any combination thereof.
  • a disclosed biotherapeutic can comprise pharmaceutical formulation comprising a probiotic, a consortium of probiotics, factors secreted from a probiotic, factors secreted from a consortium of probiotics, or any combination thereof, and a pharmaceutically acceptable carrier and/or excipient.
  • a disclosed pharmaceutical formulation can comprise at least one lyoprotectant.
  • a disclosed lyoprotectant can comprise peptone, glycerol, lactose, gelatin, glucose, sucrose, trehalose, dextran, maltodextrin, adonitol, sodium glutamate, or any combination thereof.
  • a disclosed biotherapeutic can be lyophilized or freeze- dried such that, for example, a disclosed probiotic, a disclosed consortium of probiotics, disclosed factors secreted from a probiotic, disclosed factors secreted from a consortium of probiotics, or any combination thereof are all lyophilized or freeze-dried.
  • a disclosed consortium of probiotics can comprise at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum, at least one strain from the bacterial genus Streptococcus, and at least one strain from the bacterial genus Lactobacillus.
  • a disclosed biotherapeutic can comprises one or more probiotics.
  • one or more disclosed probiotics can comprise at least one strain from the bacterial genus one Corynebacterium sp. In an aspect, one or more disclosed probiotics can comprise at least one strain from the bacterial genus Corynebacterium and at least one strain from the bacterial genus Dolosigranulum. In an aspect, one or more disclosed probiotics can comprise at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , and at least one strain from the bacterial genus Streptococcus.
  • one or more disclosed probiotics can comprise at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , and at least one strain from the bacterial genus Lactobacillus. In an aspect, one or more disclosed probiotics can comprise at least one strain from the bacterial genus Corynebacterium and at least one at least one strain from the bacterial genus Streptococcus. In an aspect, one or more disclosed probiotics can comprise at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus.
  • one or more probiotics can comprise at least one strain from the bacterial genus Corynebacterium and at least one strain from the bacterial genus Lactobacillus. In an aspect, one or more probiotics can comprise at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus.
  • a disclosed biotherapeutic can comprise one or more factors secreted by a disclosed probiotic or secreted by a disclosed consortium of probiotics.
  • a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus.
  • a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium. In an aspect of a disclosed pharmaceutical formulation, a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium and at least one strain from the bacterial genus Dolosigranulum. In an aspect of a disclosed pharmaceutical formulation, a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , and at least one train from the bacterial genus Streptococcus.
  • a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , and at least one strain from the bacterial genus Lactobacillus.
  • a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium and at least one strain from the bacterial genus Streptococcus.
  • a disclosed biotherapeutic can comprise comprises one or more factors secreted by at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus.
  • a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium and at least one strain from the bacterial genus Lactobacillus.
  • a disclosed strain from the bacterial genus Corynebacterium can comprise C. accolens , C.
  • afermentans subsp. afermentans C. afermentans subsp. lipophilum , C. ammoniagenes , C. amycolatum , C. appendicis , C. aquaticum , C. arge ntorate use, C. city pi cum, C. aurimucosum , C. auris, C. bovis, C. canis, C. confusum , C. coyleae , C. diphtheriae , C. durum , C. efficiens , C. equi (now Rhodococcus equi ), C. falsenii , C. flavescens , C. grisburgense , C.
  • a disclosed strain from the bacterial genus Corynebacterium can comprise C. accolens, C. coyleae, C. propinquum, C. pseudodiphtheriticum, C. amycolatum, C. glutamicum, C. aurimucosum, C. tuberculostearicum, C.
  • a disclosed strain from the bacterial genus Corynebacterium can comprise any species identified in Table 13 (supra).
  • a disclosed therapeutically effective dose can comprise a total of at least 100 bacterial CFUs of the one or more probiotics, a total of at least 200 to at least 300 bacterial CFUs of the one or more probiotics, a total of at least 300 to at least 400 bacterial CFUs of the one or more probiotics, a total of at least 400 to at least 500 bacterial CFUs of the one or more probiotics, a total of at least 500 to at least 600 bacterial CFUs of the one or more probiotics, a total of at least 600 to at least 700 bacterial CFUs of the one or more probiotics, a total of at least 700 to at least 800 bacterial CFUs of the one or more probiotics, a total of at least 800 to at least 900 bacterial CFUs to at least 1000 bacterial CFUs of the one or more probiotics, or a total of at least 1000 bacterial CFUs of one or more disclosed probiotics (
  • a disclosed therapeutically effective dose can comprise a total of at least 1000 to at least 2000 bacterial CFUs of the one or more probiotics, a total of at least 2000 to at least 3000 bacterial CFUs of the one or more probiotics, a total of at least 3000 to at least 4000 bacterial CFUs of the one or more probiotics, a total of at least 4000 to at least 5000 bacterial CFUs of the one or more probiotics, a total of at least 5000 to at least 6000 bacterial CFUs of the one or more probiotics, a total of at least 6000 to at least 7000 bacterial CFUs of the one or more probiotics, a total of at least 8000 to at least 9000 bacterial CFUs of the one or more probiotics, or a total of at least 10,000 bacterial CFUs of one or more disclosed probiotics (such as, for example, at least one strain from the bacterial genus Coryn
  • a disclosed therapeutically effective dose can comprise a total of at least 100 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., Lactobacillus sp., or any combination thereof, a total of at least 200 to at least 300 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., Lactobacillus sp., or any combination thereof, a total of at least 300 to at least 400 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., Lactobacillus sp., or any combination thereof, a total of at least 400 to at least 500 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp
  • Lactobacillus sp., or any combination thereof a total of at least 500 to at least 600 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., Lactobacillus sp., or any combination thereof, a total of at least 600 to at least 700 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., Lactobacillus sp., or any combination thereof, a total of at least 700 to at least 800 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., Lactobacillus sp., or any combination thereof, a total of at least 800 to at least 900 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp., Strepto
  • Lactobacillus sp. or any combination thereof, a total of at least 900 to at least 1000 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., Lactobacillus sp., or any combination thereof, or a total of at least 1000 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., Lactobacillus sp., or any combination thereof.
  • a disclosed therapeutically effective dose can comprise a total of at least 1000 to at least 2000 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., Lactobacillus sp., or any combination thereof, a total of at least 2000 to at least 3000 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 3000 to at least 4000 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp.
  • Lactobacillus sp ., or any combination thereof a total of at least 4000 to at least 5000 bacterial CFUs of the Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 5000 to at least 6000 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 6000 to at least 7000 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 8000 to at least 9000 bacterial CFUs of Corynebacterium
  • a disclosed therapeutically effective dose can comprise a total of at least 10 4 to at least 10 5 bacterial CFUs of the one or more probiotics, a total of at least 10 5 to at least 10 6 bacterial CFUs of the one or more probiotics, a total of at least 10 6 to at least 10 7 bacterial CFUs of the one or more probiotics, a total of at least 10 7 to at least 10 8 bacterial CFUs of the one or more probiotics, a total of at least 10 8 to at least 10 9 bacterial CFUs of the one or more probiotics, a total of at least 10 9 to at least 10 10 bacterial CFUs of the one or more probiotics, a total of at least 10 10 to at least 10 11 bacterial CFUs of the one or more probiotics, a total of at least 10 11 to at least 10 12 bacterial CFUs of the one or more probiotics, a total of at least 10 12 bacterial CFUs of the one or more probiotics,
  • a disclosed therapeutically effective dose can comprise at least 10 3 , 10 4 , 10 5 , 10 6 , 10 7 , 10 8 , 10 9 , 10 10 , 10 11 , or 10 12 CFUs of a disclosed probiotic or a consortium of disclosed probiotics, preferably at least 1.2 x 10 3 , 1.4 x 10 3 , 2 x 10 3 , or 3 x 10 3 CFUs of a disclosed probiotic or a consortium of disclosed probiotics, at least 5 x 10 3 , 5.02 x 10 3 , 5.04 x 10 3 , 5.2 x 10 3 , or 5.4 x 10 3 CFUs of a disclosed probiotic or a consortium of disclosed probiotics, at least 1.02 x 10 4 , 1.04 x 10 4 , 1.2 x 10 4 , 1.4 x 10 4 , 1.5 x 10 4 , 2 x 10 4 , or 3 x 10 4 CFUs of a disclosed probiotic or a consortium of disclosed probiotics, at
  • a disclosed therapeutically effective dose can comprise any amount or an unlimited amount of bacterial CFUs of the one or more probiotics.
  • a disclosed therapeutically effective dose can comprise Corynebacterium sp., Dolosigranulum sp., Streptococcus sp ., and Lactobacillus sp. in a ratio of about 1 :0.01 :0.01 :0.01 to about 1 : 1 : 1 : 1.
  • a disclosed therapeutically effective dose can comprise Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., and Lactobacillus sp. in any ratio.
  • a disclosed therapeutically effective dose can comprise a higher dose of Corynebacterium sp ., or a higher dose of Dolosigranulum sp ., or a higher dose of Streptococcus sp ., or a higher dose of Lactobacillus sp. as compared to any other bacteria in the consortium.
  • a disclosed therapeutically effective dose can comprise a dose of Lactobacillus sp. that is about double that of Corynebacterium sp.
  • a disclosed method of promoting respiratory health can further comprise treating the subject.
  • treating the subject can comprise treating the subject’s respiratory infection.
  • treating the subject can comprise treating the subject’s non- respiratory infection.
  • a disclosed method of promoting respiratory health can comprise further comprising administering to the subject a therapeutically effective amount of one or more anti- bacterial agents.
  • Anti -bacterial agents and combinations of anti-bacterial agents are known to the art and discussed supra in Part VII(C)(1).
  • a disclosed method of promoting respiratory health can further comprise administering to the subject a therapeutically effective amount of (i) one or more active agents, (ii) one or more biologically active agents, (iii) one or more pharmaceutically active agents, (iv) one or more immune-based therapeutic agents, (v) one or more clinically approved agents, or (vi) any combination thereof.
  • the dose of an active agent, a biologically active agent, a pharmaceutically active agent, an immune-based therapeutic active agent, a clinically approved agent, or an anti -bacterial agent can be about 1 ng/kg body weight/day to about 100 ng/kg body weight/day, about 10 ng/kg body weight/day to about 1 pg/kg body, about 100 ng/kg body weight/day to about 10 pg/kg body, about 1 pg/kg body weight/day to about 100 pg/kg body, about 10 pg/kg body weight/day to about 1 mg/kg body, or about 100 pg/kg body weight/day to about 10 mg/kg body.
  • administering a disclosed agent can comprise systemic or direct administration.
  • administering a disclosed anti -bacterial agent can comprise oral administration, intravenous administration, intranasal administration, intraperitoneal administration, or any combination thereof.
  • administering a disclosed agent can be administered by any method of administration disclosed herein.
  • a disclosed agent can be administered via multiple routes either concurrently or sequentially. A skilled clinician can determine the best route of administration for a disclosed agent to a subject at a given time.
  • a disclosed agent can inherently encompass a pharmaceutically acceptable salt thereof.
  • a disclosed method of promoting respiratory health can further comprise increasing the relative abundance of one or more probiotics in the subject’s microbiome.
  • a disclosed method of promoting respiratory health can further comprise increasing the relative abundance of one or more of Corynebacterium sp., Dolosigranulum sp., Streptococcus sp ., and Lactobacillus sp. in the subject’s microbiome.
  • a disclosed method of promoting respiratory health can further comprise increasing the relative abundance of one or more of at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus , or any combination thereof in the subject’s microbiome.
  • a disclosed method of promoting respiratory health can further comprise increasing the relative abundance of at least one strain from the bacterial genus Corynebacterium in the subject’s microbiome.
  • a disclosed method of promoting respiratory health can further comprise increasing the relative abundance of at least one strain from the bacterial genus Dolosigranulum in the subject’s microbiome. In an aspect, a disclosed method of promoting respiratory health can further comprise increasing the relative abundance of at least one strain from the bacterial genus Streptococcus in the subject’s microbiome. In an aspect, a disclosed method of promoting respiratory health can further comprise increasing the relative abundance of at least one strain from the bacterial genus Lactobacillus in the subject’s microbiome.
  • a disclosed method of promoting respiratory health can further comprise decreasing the relative abundance of one or more pathogenic bacteria in the subject’s microbiome.
  • a disclosed method of promoting respiratory health can further comprise decreasing the relative abundance of S. pneumoniae in the subject’s microbiome.
  • a disclosed method of promoting respiratory health can further comprise decreasing the relative abundance of S. aureus in the subject’s microbiome.
  • a disclosed method of promoting respiratory health can further comprise decreasing the relative abundance of Haemophilus influenzae and/or Moraxella catarrhalis in the subject’s microbiome.
  • a disclosed method of promoting respiratory health can further comprise administering to the subject one or more therapeutic agents.
  • a disclosed therapeutic agent can comprise a biologically active agent, a pharmaceutically active agent, an anti -bacterial agent, an anti-fungal agent, an anti-viral agent, a corticosteroid, an analgesic, an immunostimulant, an immune-based product, or any combination thereof.
  • administering can comprise intranasal administration, oral administration, sublingual administration, or any combination thereof.
  • a subject in an aspect of a disclosed method of promoting respiratory health, can be a healthy subject, for example, a subject that does not have an infection and/or is not suspected of having an infection.
  • a subject can be an adult, a child, or an infant. In an aspect, a subject can be a neonate. In an aspect, a subject can be a premature infant. In an aspect, a subject can be immune- compromised. In an aspect, a subject can have diabetes or a chronic disease (e.g., heart disease, kidney disease, or liver disease). In an aspect, a subject can have HIV. In an aspect, a subject can have cancer or has had cancer. In an aspect, a subject can be the recipient of one or more solid organ transplants. In an aspect, a subject can have nephrotic syndrome. In an aspect, a subject can be alcoholic or can smoke cigarettes. In an aspect, a subject can have a chronic lung disease. In an aspect, a disclosed chronic lung disease can comprise emphysema, chronic obstructive lung disease, chronic obstructive pulmonary disease, asthma, or any combination thereof.
  • a chronic lung disease can comprise emphysema, chronic obstructive lung disease
  • a subject can be diagnosed with an infection of one or more parts of the respiratory system. In an aspect, a subject can be suspected of having an infection in one or more parts of the respiratory system. In an aspect, a disclosed therapeutically effective amount of a biotherapeutic can comprise an amount sufficient to inhibit and/or prevent the growth of one or more pathogenic bacteria in one or more parts of the subject’s respiratory system. In an aspect, a disclosed therapeutically effective amount of a biotherapeutic can comprise an amount sufficient to inhibit and/or prevent the spread of one or more pathogenic bacteria from a first part of the subject’s respiratory system to a second part of the subject’s respiratory system.
  • one or more disclosed probiotics can inhibit and/or prevent the growth and/or spread of one or more pathogenic bacteria using competitive adherence and/or non-adherence mechanisms (e.g., secretion of antimicrobial factors). In an aspect, one or more disclosed probiotics can inhibit and/or prevent the adherence and/or colonization of one or more pathogenic bacteria. In an aspect, one or more disclosed probiotics can modulate the endocytosis or paracellular migration of one or more pathogenic bacteria. In an aspect, one or more disclosed probiotics can inhibit and/or prevent the spread of one or more pathogenic bacteria by competitive adherence and/or niche occupancy.
  • one or more disclosed probiotics can inhibit and/or prevent the growth and/or spread of S. pneumoniae using competitive adherence and/or non-adherence mechanisms (e.g., secretion of antimicrobial factors). In an aspect, one or more disclosed probiotics can inhibit and/or prevent the adherence and/or colonization of S. pneumoniae. In an aspect, one or more disclosed probiotics can modulate the endocytosis or paracellular migration of S. pneumoniae. In an aspect, one or more disclosed probiotics can inhibit and/or prevent the spread S. pneumoniae by competitive adherence and/or niche occupancy.
  • one or more disclosed probiotics can secrete one or more factors.
  • a disclosed secreted factor can be species-dependent and/or strain-dependent.
  • a disclosed secreted factor can inhibit and/or prevent the growth and/or spread of one or more pathogenic bacteria.
  • a disclosed secreted factor can inhibit and/or prevent the adherence and/or colonization of one or more pathogenic bacteria.
  • a disclosed secreted factor can modulate the endocytosis or paracellular migration of one or more pathogenic bacteria.
  • a disclosed secreted factor can inhibit and/or prevent the spread of one or more pathogenic bacteria by competitive adherence and/or niche occupancy.
  • a disclosed secreted factor can inhibit and/or prevent the growth and/or spread of S. pneumoniae. In an aspect, a disclosed secreted factor can inhibit and/or prevent the adherence and/or colonization of S. pneumoniae. In an aspect, a disclosed secreted factor can modulate the endocytosis or paracellular migration of S. pneumoniae. In an aspect, a disclosed secreted factor can inhibit and/or prevent the spread of S. pneumoniae by competitive adherence and/or niche occupancy.
  • Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof can secrete one or more secreted factors that modulate the endocytosis or paracellular migration of one or more pathogenic bacteria.
  • a disclosed method of promoting respiratory health Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof can secrete one or more secreted factors inhibit and/or prevent the spread of one or more pathogenic bacteria by competitive adherence and/or niche occupancy.
  • a disclosed method of promoting respiratory health Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof can secrete one or more secreted factors inhibit and/or prevent the growth and/or spread of S. pneumoniae.
  • Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof can secrete one or more factors inhibit and/or prevent the adherence and/or colonization of S. pneumoniae.
  • one or more factors can modulate the endocytosis or paracellular migration of S. pneumoniae.
  • Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof can secrete one or more factors inhibit and/or prevent the spread of S. pneumoniae by competitive adherence and/or niche occupancy.
  • Corynebacterium sp. can secrete one or more factors that inhibit and/or prevent the growth and/or spread of one or more pathogenic bacteria. In an aspect of a disclosed method of promoting respiratory health, Corynebacterium sp. can secrete one or more factors that inhibit and/or prevent the adherence and/or colonization of one or more pathogenic bacteria. In an aspect of a disclosed method of promoting respiratory health, Corynebacterium sp. can secrete one or more secreted factors that modulate the endocytosis or paracellular migration of one or more pathogenic bacteria. In an aspect of a disclosed method of promoting respiratory health, Corynebacterium sp. can secrete one or more secreted factors that inhibit and/or prevent the spread of one or more pathogenic bacteria by competitive adherence and/or niche occupancy.
  • Corynebacterium sp. can secrete one or more secreted factors that inhibit and/or prevent the growth and/or spread of S. pneumoniae. In an aspect of a disclosed method of promoting respiratory health, Corynebacterium sp. can secrete one or more factors that inhibit and/or prevent the adherence and/or colonization of S. pneumoniae. In an aspect of a disclosed method of promoting respiratory health, Corynebacterium sp. can secrete one or more factors that modulate the endocytosis or paracellular migration of S. pneumoniae. In an aspect of a disclosed method of promoting respiratory health, Corynebacterium sp. can secrete one or more factors that inhibit and/or prevent the spread of S. pneumoniae by competitive adherence and/or niche occupancy.
  • a disclosed method of promoting respiratory health can comprise a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any amount of inhibiting and/or preventing the growth and/or spread of one or more pathogenic bacteria (e.g., S. pneumoniae ) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • a disclosed method of promoting respiratory health can comprise a 10-20%, 20-30%, 30-40%, 40-50%, 50-60%, 60-70%, 70-80%, 80-90%, or 90-100% or any amount of inhibiting and/or preventing the growth and/or spread of one or more pathogenic bacteria (e.g., S. pneumoniae) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • a disclosed method of promoting respiratory health can comprise a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any amount of inhibiting and/or preventing the adherence and/or colonization of one or more pathogenic bacteria (e.g., S. pneumoniae) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • pathogenic bacteria e.g., S. pneumoniae
  • a disclosed method of promoting respiratory health can comprise a 10-20%, 20-30%, 30-40%, 40-50%, 50-60%, 60-70%, 70-80%, 80-90%, or 90-100% or any amount of inhibiting and/or preventing the adherence and/or colonization of one or more pathogenic bacteria (e.g., S. pneumoniae ) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • pathogenic bacteria e.g., S. pneumoniae
  • a disclosed method of promoting respiratory health can comprise a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any amount of modulating the endocytosis or paracellular migration of one or more pathogenic bacteria (e.g., S. pneumoniae ) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • a disclosed method of promoting respiratory health can comprise a 10-20%, 20-30%, 30-40%, 40-50%, 50-60%, 60-70%, 70-80%, 80-90%, or 90-100% or any amount of modulating the endocytosis or paracellular migration of one or more pathogenic bacteria (e.g., S. pneumoniae) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • a disclosed method of promoting respiratory health can comprise a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any amount of inhibiting and/or preventing the spread of one or more pathogenic bacteria (e.g., S. pneumoniae ) by competitive adherence and/or niche occupancy when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • pathogenic bacteria e.g., S. pneumoniae
  • a disclosed method of promoting respiratory health can comprise a 10-20%, 20-30%, 30-40%, 40-50%, 50-60%, 60- 70%, 70-80%, 80-90%, or 90-100% or any amount of inhibiting and/or preventing the spread of one or more pathogenic bacteria (e.g., S. pneumoniae ) by competitive adherence and/or niche occupancy when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • pathogenic bacteria e.g., S. pneumoniae
  • a control subject such as, for example, a subject that has not received a disclosed biotherapeutic
  • a disclosed method of promoting respiratory health can comprise repeating the administering of one or more disclosed biotherapeutics, one or more disclosed secreted factors, a disclosed consortium of probiotics, one or more disclosed probiotics, or any combination thereof.
  • repeating the administering can comprise administering one or more times daily (e.g., 1, 2, 3, or 4 times).
  • repeating the administering can comprise administering on several consecutive days (e.g., for 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 days, or more than 10 days), weeks (e.g., for 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 weeks, or more than 10 weeks), or months (e.g., for 1, 2, 3, 4, 5, or 6 months, or more than 6 months).
  • a disclosed biotherapeutic, a disclosed secreted factor, a disclosed consortium of probiotics, a disclosed probiotic, or any combination thereof can be administered 1 - 3 times per day for about 7 to 21 days.
  • a disclosed method of promoting respiratory health can comprise monitoring the subject.
  • monitoring the subject can comprise monitoring the subject for the development of adverse effects.
  • a disclosed method can comprise continuing to treat the subject.
  • continuing to treat the subject can comprise continuing to administer to the subject one or more disclosed biotherapeutics, one or more disclosed secreted factors, a disclosed consortium of probiotics, one or more disclosed probiotics, or any combination thereof.
  • a disclosed method in the presence of adverse effects, can comprise modifying one or more steps of the method.
  • modifying one or more steps of a disclosed method can comprise modifying the administering step.
  • modifying the administering step can comprise changing the amount of one or more disclosed biotherapeutics, one or more disclosed secreted factors, a disclosed consortium of probiotics, one or more disclosed probiotics, or any combination thereof administered to the subject, changing the frequency of administration of one or more disclosed biotherapeutics, one or more disclosed secreted factors, a disclosed consortium of probiotics, one or more disclosed probiotics, or any combination thereof, changing the duration of administration of one or more disclosed biotherapeutics, one or more disclosed secreted factors, a disclosed consortium of probiotics, one or more disclosed probiotics, or any combination thereof, changing the route of administration of one or more disclosed biotherapeutics, one or more disclosed secreted factors, a disclosed consortium of probiotics, one or more disclosed probiotics, or any combination thereof, or any combination of disclosed changes.
  • a disclosed method of promoting respiratory health can comprise manipulating the microbiome to inhibit and/or prevent infection caused by one or more pathogenic bacteria, such as an infection caused by S. pneumoniae.
  • a disclosed method of promoting respiratory health can comprise manipulating the microbiome to decrease and/or minimize the risk of infection caused by one or more pathogenic bacteria, such as an infection caused by S. pneumoniae. For example, in an aspect, when the relative abundance of one or more disclosed Corynebacterium sp. is below a threshold level of 1.2 x 10 6 16S rRNA gene copies per biological sample, then the risk of colonization by S. pneumoniae is increased and/or higher and/or enhanced.
  • a disclosed method can further comprise administering and/or continuing to administer a therapeutically effective amount of a disclosed biotherapeutic.
  • a disclosed method can further comprise continuing to monitor the subject.
  • the relative abundance of one or more disclosed Corynebacterium sp. when the relative abundance of one or more disclosed Corynebacterium sp. is less than about 50%, about 60%, about 70%, about 80%, or 90% of the microbiome, then the risk of colonization by S. pneumoniae is increased and/or higher and/or enhanced.
  • the relative abundance of one or more disclosed Corynebacterium sp. when the relative abundance of one or more disclosed Corynebacterium sp. is about 50% to about 60%, about 60% to about 70%, about 70% to about 80%, about 80% to about 90% of the microbiome, then the risk of colonization by S. pneumoniae is increased and/or higher and/or enhanced.
  • a disclosed method can further comprise administering and/or continuing to administer a therapeutically effective amount of a disclosed biotherapeutic.
  • a disclosed method can further comprise administering and/or continuing to administer a therapeutically effective amount of a disclosed biotherapeutic.
  • a disclosed method can further comprise administering and/or continuing to administer a therapeutically effective amount of a disclosed biotherapeutic.
  • when the relative abundance of Corynebacterium sp. is less than about 50%, about 60%, about 70%, about 80%, or 90% of the microbiome, then a disclosed method can further comprise administering and/or continuing to administer a therapeutically effective amount of a disclosed biotherapeutic.
  • the relative abundance of Corynebacterium sp. when the relative abundance of Corynebacterium sp.
  • a disclosed method can further comprise continuing to monitor the subject.
  • a disclosed method can further comprise continuing to monitor the subject.
  • a disclosed method can comprise subjecting the subject to one or more invasive or non-invasive diagnostic assessments. Diagnostic assessments are known to the art.
  • a disclosed non-invasive diagnostic assessment can comprise x-rays, computerized tomography (CT) scans, magnetic resonance imaging (MRI) scans, ultrasounds, positron emission tomography (PET) scans, or any combination thereof.
  • a disclosed invasive diagnostic assessment can comprise a tissue biopsy or exploratory surgery.
  • techniques to monitor, measure, and/or assess the restoring one or more aspects of respiratory health can comprise qualitative (or subjective) means as well as quantitative (or objective) means. These means are known to the skilled person. For example, representative regulated variables and sensors relating to systemic homeostasis are provided below.
  • a disclosed biotherapeutic, a disclosed secreted factor, a disclosed consortium of probiotics, a disclosed probiotic, or any combination thereof can be administered in the absence of identifying the one or more pathogenic bacteria and/or in the absence of characterizing the microbiome.
  • a disclosed biotherapeutic, a disclosed secreted factor, a disclosed consortium of probiotics, a disclosed probiotic, or any combination thereof can be administered on demand.
  • a disclosed biotherapeutic can be formulated for administration as a pharmaceutical formulation.
  • a disclosed pharmaceutical formulation comprising a probiotic, a consortium of probiotics, factors secreted from a probiotic, factors secreted from a consortium of probiotics, or any combination thereof, and a pharmaceutically acceptable carrier and/or excipient can be used in any disclosed method of promoting respiratory health.
  • Any pharmaceutical formulation disclosed herein can be used in a disclosed method of promoting respiratory health.
  • Disclosed herein is a method of reducing the risk of developing a pathogenic bacterial infection, the method comprising administering to a subject in need thereof a therapeutically effective amount of a biotherapeutic, thereby preventing and/or inhibiting the colonization of the pathogenic bacteria.
  • Disclosed herein is a method of reducing the risk of developing a S. pneumoniae infection, the method comprising administering to a subject in need thereof a therapeutically effective amount of a biotherapeutic, thereby preventing and/or inhibiting the colonization of S. pneumoniae.
  • a subject in an aspect of a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection, can be any subject. In an aspect, a subject that does not have an infection and/or is not suspected of having an infection.
  • the colonization of a pathogenic bacteria and/or S. pneumoniae in the subject’s respiratory system can be inhibited and/or prevented.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can further comprise promoting respiratory health in a subject.
  • a disclosed biotherapeutic can inhibit and/or prevent the growth of one or more pathogenic bacteria and/or S. pneumoniae in one or more parts of the subject’s respiratory system.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can further comprise characterizing the microbiome of a biological sample.
  • a disclosed microbiome can comprise the nasopharyngeal microbiome, the nasal microbiome, or both.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can further comprise obtaining a biological sample from the subject.
  • a disclosed biological sample can comprise a nasal swab or lavage, a nasopharyngeal swab or lavage, or a pharyngeal swab or lavage, or any combination thereof.
  • a disclosed biological sample can comprise nasal secretion and/or cough droplets.
  • characterizing the microbiome can comprise (i) collecting a biological sample from the subject; (ii) extracting nucleic acid from the subject’s biological sample; and (iii) sequencing the extracted nucleic acid.
  • sequencing the extracted nucleic acid can generate sequence data.
  • characterizing the microbiome can further comprise analyzing the sequence data using taxonomic classification.
  • using taxonomic classification can comprise PCR amplification.
  • PCR amplification can comprise using primers targeting the 16S rRNA gene.
  • PCR amplification can comprise primers targeting the V4 variable region of the 16S rRNA gene.
  • disclosed primers can comprise a pair of primers.
  • a disclosed pair of primers can comprise a primer having the sequence of SEQ ID NO:01 and a primer having the sequence of SEQ ID NO:02. In an aspect, a disclosed pair of primers can comprise a primer having the sequence of SEQ ID NO:03 and a primer having the sequence of SEQ ID NO:04. In an aspect, a disclosed pair of primers can comprise a primer having the sequence of SEQ ID NO:05 and a primer having the sequence of SEQ ID NO:06.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can further comprise identifying the one or more pathogenic bacteria.
  • the disclosed pathogenic bacteria can comprise Streptococcus sp.
  • Streptococcus sp. can comprise S. pneumoniae.
  • the disclosed pathogenic bacteria can comprise Staphylococcus sp.
  • Staphylococcus sp. can comprise methicillin-sensitive S. aureus or methicillin-resistant S. aureus.
  • the disclosed pathogenic bacteria can comprise Haemophilus influenzae or Moraxella catarrhalis.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can further comprise diagnosing the subject with an infection.
  • a diagnosed infection can comprise a respiratory infection.
  • a diagnosed infection can affect the subject’s mouth, nose, ears, sinuses, pharynx, trachea, bronchial tubes, lungs, alveoli, bronchioles, capillaries, lung lobes, pleura, cilia, epiglottis, larynx, or any combination thereof.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can further comprise diagnosing the subject with pneumonia, otitis media, sinusitis, rhinosinusitis, or any combination thereof.
  • otitis media can be considered a general term for middle-ear inflammation and can be classified clinically as acute otitis media (AOM), recurrent AOM, OM with effusion (OME), or chronic OME, chronic suppurative OM (CSOM), or middle ear effusion (MEE) (discussed supra).
  • sinusitis can occur when the tissue lining of the sinuses becomes swollen or inflamed.
  • Sinusitis can comprise acute sinusitis (e.g., when symptoms are present for 4 weeks or less), chronic sinusitis (e.g., when the swelling of the sinuses is present for longer than 3 months), or subacute sinusitis (e.g., when the swelling is present between one and three months).
  • rhinosinusitis can occur when the mucosal lining in the paranasal sinuses and nasal cavity becomes inflamed. Most cases of acute rhinosinusitis are caused by viral upper respiratory infections.
  • a disclosed biotherapeutic can comprise a probiotic, a consortium of probiotics, factors secreted from a probiotic, factors secrete from a consortium of probiotics, or any combination thereof.
  • a disclosed biotherapeutic can comprise pharmaceutical formulation comprising a probiotic, a consortium of probiotics, factors secreted from a probiotic, factors secreted from a consortium of probiotics, or any combination thereof, and a pharmaceutically acceptable carrier and/or excipient.
  • a disclosed pharmaceutical formulation can comprise at least one lyoprotectant.
  • a disclosed lyoprotectant can comprise peptone, glycerol, lactose, gelatin, glucose, sucrose, trehalose, dextran, maltodextrin, adonitol, sodium glutamate, or any combination thereof.
  • a disclosed biotherapeutic can be lyophilized or freeze-dried such that, for example, a disclosed probiotic, a disclosed consortium of probiotics, disclosed factors secreted from a probiotic, disclosed factors secrete from a consortium of probiotics, or any combination thereof are all lyophilized or freeze-dried.
  • a disclosed biotherapeutic can comprise one or more probiotics.
  • a disclosed consortium of probiotics can comprise at least one strain from the bacterial genus Corynebacterium, at least one strain from the bacterial genus Dolosigranulum , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus.
  • the at least one strain from the bacterial genus Cory neb acterium can comprise one or more strains of Corynebacterium accolens.
  • the at least one strain from the bacterial genus Dolosigranulum can comprise one or more strains of Dolosigranulum pigrum.
  • the at least one strain from the bacterial genus Streptococcus can comprise one or more strains of Streptococcus mitis, Streptococcus salivarius , Streptococcus oralis , or Streptococcus thermophilus .
  • the at least one strain from the bacterial genus Lactobacillus can comprise one or more strains of Lactobacillus rhamnosus or Lactobacillus acidophilus.
  • one or more disclosed probiotics can comprise at least one strain from the bacterial genus one Corynebacterium sp. In an aspect, one or more disclosed probiotics can comprise at least one strain from the bacterial genus Corynebacterium and at least one strain from the bacterial genus Dolosigranulum. In an aspect, one or more disclosed probiotics can comprise at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , and at least one strain from the bacterial genus Streptococcus.
  • one or more disclosed probiotics can comprise at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , and at least one strain from the bacterial genus Lactobacillus. In an aspect, one or more disclosed probiotics can comprise at least one strain from the bacterial genus Corynebacterium and at least one at least one strain from the bacterial genus Streptococcus. In an aspect, one or more disclosed probiotics can comprise at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus.
  • one or more probiotics can comprise at least one strain from the bacterial genus Corynebacterium and at least one strain from the bacterial genus Lactobacillus. In an aspect, one or more probiotics can comprise at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus.
  • a disclosed biotherapeutic can comprise one or more factors secreted by a disclosed probiotic or secreted by a disclosed consortium of probiotics.
  • a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus.
  • a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium. In an aspect, a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium and at least one strain from the bacterial genus Dolosigranulum. In an aspect, a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , and at least one train from the bacterial genus Streptococcus.
  • a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , and at least one strain from the bacterial genus Lactobacillus. In an aspect, a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium and at least one strain from the bacterial genus Streptococcus.
  • a disclosed biotherapeutic can comprise comprises one or more factors secreted by at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus.
  • a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium and at least one strain from the bacterial genus Lactobacillus.
  • a disclosed Corynebacterium can comprise C. accolens , C. afermentans subsp. afermentans , C. afermentans subsp.
  • a disclosed strain from the bacterial genus Corynebacterium can comprise C. accolens , C. coyleae , C. propinquum , C. pseudodiphtheriticum , C. amycolatum , C. glutamicum , C.
  • a disclosed strain from the bacterial genus Corynebacterium can comprise any species identified in Table 13.
  • a disclosed therapeutically effective dose can comprise a total of at least 100 bacterial CFUs of the one or more probiotics, a total of at least 200 to at least 300 bacterial CFUs of the one or more probiotics, a total of at least 300 to at least 400 bacterial CFUs of the one or more probiotics, a total of at least 400 to at least 500 bacterial CFUs of the one or more probiotics, a total of at least 500 to at least 600 bacterial CFUs of the one or more probiotics, a total of at least 600 to at least 700 bacterial CFUs of the one or more probiotics, a total of at least 700 to at least 800 bacterial CFUs of the one or more probiotics, a total of at least 800 to at least 900 bacterial CFUs of the one or more probiotics, a total of at least 900 to at least 1000 bacterial CFUs of the one or more probiotics, a total of at least 100 bacterial CFUs of the one or more probiotics,
  • a disclosed therapeutically effective dose can comprise a total of at least 1000 to at least 2000 bacterial CFUs of the one or more probiotics, a total of at least 2000 to at least 3000 bacterial CFUs of the one or more probiotics, a total of at least 3000 to at least 4000 bacterial CFUs of the one or more probiotics, a total of at least 4000 to at least 5000 bacterial CFUs of the one or more probiotics, a total of at least 5000 to at least 6000 bacterial CFUs of the one or more probiotics, a total of at least 6000 to at least 7000 bacterial CFUs of the one or more probiotics, a total of at least 8000 to at least 9000 bacterial CFUs of the one or more probiotics, or a total of at least 10,000 bacterial CFUs of one or more disclosed probiotics (such as, for
  • a disclosed therapeutically effective dose can comprise a total of at least 100 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp., or any combination thereof, a total of at least 200 to at least 300 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 300 to at least 400 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 400 to at least
  • Lactobacillus sp ., or any combination thereof a total of at least 600 to at least 700 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 700 to at least 800 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 800 to at least 900 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 900 to at least 1000 bacterial CFUs of Corynebacterium sp .
  • a disclosed therapeutically effective dose can comprise a total of at least 1000 to at least 2000 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp.
  • Lactobacillus sp ., or any combination thereof a total of at least 2000 to at least 3000 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 3000 to at least 4000 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 4000 to at least 5000 bacterial CFUs of the Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 5000 to at least 6000 bacterial CFUs of Corynebacterium
  • Lactobacillus sp . or any combination thereof, a total of at least 8000 to at least 9000 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, or a total of at least 10,000 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof. [0164] In an aspect of a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S.
  • a disclosed therapeutically effective dose can comprise a total of at least 10 4 to at least 10 5 bacterial CFUs of the one or more probiotics, a total of at least 10 5 to at least 10 6 bacterial CFUs of the one or more probiotics, a total of at least 10 6 to at least 10 7 bacterial CFUs of the one or more probiotics, a total of at least 10 7 to at least 10 8 bacterial CFUs of the one or more probiotics, a total of at least 10 8 to at least 10 9 bacterial CFUs of the one or more probiotics, a total of at least 10 9 to at least 10 10 bacterial CFUs of the one or more probiotics, a total of at least 10 10 to at least 10 11 bacterial CFUs of the one or more probiotics, a total of at least 10 11 to at least 10 12 bacterial CFUs of the one or more probiotics, a total of at least 10 12 bacterial CFUs of the one or more probiotics, or more than 10
  • a disclosed therapeutically effective dose can comprise at least 10 3 , 10 4 , 10 5 ,
  • a disclosed therapeutically effective dose can comprise Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., and Lactobacillus sp. in a ratio of about 1:0.01:0.01:0.01 to about 1 : 1 : 1 : 1.
  • a disclosed therapeutically effective dose can comprise Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., and Lactobacillus sp. in any ratio.
  • a disclosed therapeutically effective dose can comprise a higher dose of Corynebacterium sp ., or a higher dose of Dolosigranulum sp ., or a higher dose of Streptococcus sp ., or a higher dose of Lactobacillus sp. as compared to any other bacteria in the consortium.
  • a disclosed therapeutically effective dose can comprise a dose of Lactobacillus sp. that is about double that of Corynebacterium sp.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can further comprise treating the subject.
  • treating the subject can comprise treating the subject’s respiratory infection.
  • treating the subject can comprise treating the subject’s non-respiratory infection.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can comprise further comprising administering to the subject a therapeutically effective amount of one or more anti -bacterial agents.
  • Anti -bacterial agents and combinations of anti -bacterial agents are known to the art and discussed supra in Part VII(C)(1).
  • pneumoniae infection can comprise further comprising administering to the subject a therapeutically effective amount of (i) one or more active agents, (ii) one or more biologically active agents, (iii) one or more pharmaceutically active agents, (iv) one or more immune-based therapeutic agents, (v) one or more clinically approved agents, or (vi) any combination thereof.
  • a therapeutically effective amount of an active agent, a biologically active agent, a pharmaceutically active agent, an immune-based therapeutic active agent, a clinically approved agent, or an anti -bacterial agent can be about 1 ng/kg body weight/day to about 100 ng/kg body weight/day, about 10 ng/kg body weight/day to about 1 pg/kg body, about 100 ng/kg body weight/day to about 10 pg/kg body, about 1 pg/kg body weight/day to about 100 pg/kg body, about 10 pg/kg body weight/day to about 1 mg/kg body, or about 100 pg/kg body weight/day to about 10 mg/kg body.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can further comprise increasing the relative abundance of one or more probiotics in the subject’s microbiome.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can further comprise increasing the relative abundance of one or more of Corynebacterium sp., Dolosigranulum sp., Streptococcus sp ., and Lactobacillus sp. in the subject’s microbiome.
  • pneumoniae infection can further comprise increasing the relative abundance of one or more of at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus , or any combination thereof in the subject’s microbiome.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can further comprise increasing the relative abundance of at least one strain from the bacterial genus Corynebacterium in the subject’s microbiome.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can further comprise increasing the relative abundance of at least one strain from the bacterial genus Dolosigranulum in the subject’s microbiome.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can further comprise increasing the relative abundance of at least one strain from the bacterial genus Streptococcus in the subject’s microbiome.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can further comprise increasing the relative abundance of at least one strain from the bacterial genus Lactobacillus in the subject’s microbiome.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can further comprise decreasing the relative abundance of one or more pathogenic bacteria in the subject’s microbiome.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can further comprise decreasing the relative abundance of S. pneumoniae in the subject’s microbiome.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can further comprise decreasing the relative abundance of a S. aureus in the subject’s microbiome.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can further comprise administering to the subject one or more therapeutic agents.
  • a disclosed therapeutic agent can comprise a biologically active agent, a pharmaceutically active agent, an anti-bacterial agent, an anti-fungal agent, an anti-viral agent, a corticosteroid, an analgesic, an immunostimulant, an immune-based product, or any combination thereof.
  • administering can comprise intranasal administration, oral administration, sublingual administration, or any combination thereof.
  • a subj ect can be a healthy subj ect, for example, a subj ect that does not have an infection and/or is not suspected of having an infection.
  • a subject can be an adult, a child, or an infant. In an aspect, a subject can be a neonate. In an aspect, a subject can be a premature infant. In an aspect, a subject can be immune- compromised. In an aspect, a subject can have diabetes or a chronic disease (e.g., heart disease, kidney disease, or liver disease). In an aspect, a subject can have HIV. In an aspect, a subject can have cancer or has had cancer. In an aspect, a subject can be the recipient of one or more solid organ transplants. In an aspect, a subject can have nephrotic syndrome. In an aspect, a subject can be alcoholic or can smoke cigarettes. In an aspect, a subject can have a chronic lung disease. In an aspect, a disclosed chronic lung disease can comprise emphysema, chronic obstructive lung disease, chronic obstructive pulmonary disease, asthma, or any combination thereof.
  • a chronic lung disease can comprise emphysema, chronic obstructive lung disease
  • a subject can be diagnosed with an infection of one or more parts of the respiratory system. In an aspect, a subject can be suspected of having an infection in one or more parts of the respiratory system. In an aspect, a disclosed therapeutically effective amount of a biotherapeutic can comprise an amount sufficient to inhibit and/or prevent the growth of one or more pathogenic bacteria in one or more parts of the subject’s respiratory system. In an aspect, a disclosed therapeutically effective amount of a biotherapeutic can comprise an amount sufficient to inhibit and/or prevent the spread of one or more pathogenic bacteria from a first part of the subject’s respiratory system to a second part of the subject’s respiratory system.
  • one or more disclosed probiotics can inhibit and/or prevent the growth and/or spread of one or more pathogenic bacteria using competitive adherence and/or non-adherence mechanisms (e.g., secretion of antimicrobial factors). In an aspect, one or more disclosed probiotics can inhibit and/or prevent the adherence and/or colonization of one or more pathogenic bacteria. In an aspect, one or more disclosed probiotics can modulate the endocytosis or paracellular migration of one or more pathogenic bacteria. In an aspect, one or more disclosed probiotics can inhibit and/or prevent the spread of one or more pathogenic bacteria by competitive adherence and/or niche occupancy.
  • one or more disclosed probiotics can inhibit and/or prevent the growth and/or spread of S. pneumoniae using competitive adherence and/or non-adherence mechanisms (e.g., secretion of antimicrobial factors). In an aspect, one or more disclosed probiotics can inhibit and/or prevent the adherence and/or colonization of S. pneumoniae. In an aspect, one or more disclosed probiotics can modulate the endocytosis or paracellular migration of S. pneumoniae. In an aspect, one or more disclosed probiotics can inhibit and/or prevent the spread S. pneumoniae by competitive adherence and/or niche occupancy.
  • one or more disclosed probiotics can secrete one or more factors.
  • a disclosed secreted factor can be species-dependent and/or strain-dependent.
  • a disclosed secreted factor can inhibit and/or prevent the growth and/or spread of one or more pathogenic bacteria.
  • a disclosed secreted factor can inhibit and/or prevent the adherence and/or colonization of one or more pathogenic bacteria.
  • a disclosed secreted factor can modulate the endocytosis or paracellular migration of one or more pathogenic bacteria.
  • a disclosed secreted factor can inhibit and/or prevent the spread of one or more pathogenic bacteria by competitive adherence and/or niche occupancy.
  • a disclosed secreted factor can inhibit and/or prevent the growth and/or spread of S. pneumoniae.
  • a disclosed secreted factor can inhibit and/or prevent the adherence and/or colonization of S. pneumoniae.
  • a disclosed secreted factor can modulate the endocytosis or paracellular migration of S. pneumoniae.
  • a disclosed secreted factor can inhibit and/or prevent the spread of S. pneumoniae by competitive adherence and/or niche occupancy.
  • pneumoniae infection can secrete one or more factors that inhibit and/or prevent the adherence and/or colonization of one or more pathogenic bacteria.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can secrete one or more secreted factors that modulate the endocytosis or paracellular migration of one or more pathogenic bacteria.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof can secrete one or more secreted factors inhibit and/or prevent the spread of one or more pathogenic bacteria by competitive adherence and/or niche occupancy.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S can secrete one or more secreted factors inhibit and/or prevent the spread of one or more pathogenic bacteria by competitive adherence and/or niche occupancy.
  • pneumoniae infection corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof can secrete one or more secreted factors inhibit and/or prevent the growth and/or spread of S. pneumoniae.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof can secrete one or more factors inhibit and/or prevent the adherence and/or colonization of S. pneumoniae.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection, Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof secrete one or more factors can modulate the endocytosis or paracellular migration of S. pneumoniae.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S can modulate the endocytosis or paracellular migration of S. pneumoniae.
  • pneumoniae infection corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof can secrete one or more factors inhibit and/or prevent the spread of S. pneumoniae by competitive adherence and/or niche occupancy.
  • Corynebacterium sp. can secrete one or more factors that inhibit and/or prevent the growth and/or spread of one or more pathogenic bacteria. In an aspect of a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection, Corynebacterium sp. can secrete one or more factors that inhibit and/or prevent the adherence and/or colonization of one or more pathogenic bacteria. In an aspect of a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection, Corynebacterium sp.
  • Corynebacterium sp. can secrete one or more secreted factors that modulate the endocytosis or paracellular migration of one or more pathogenic bacteria.
  • Corynebacterium sp. can secrete one or more secreted factors that inhibit and/or prevent the spread of one or more pathogenic bacteria by competitive adherence and/or niche occupancy.
  • Corynebacterium sp. can secrete one or more secreted factors that inhibit and/or prevent the growth and/or spread of S. pneumoniae.
  • Corynebacterium sp. can secrete one or more factors that inhibit and/or prevent the adherence and/or colonization of S. pneumoniae. In an aspect of a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection, Corynebacterium sp. can secrete one or more factors that modulate the endocytosis or paracellular migration of S. pneumoniae. In an aspect of a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection, Corynebacterium sp. can secrete one or more factors that inhibit and/or prevent the spread of S. pneumoniae by competitive adherence and/or niche occupancy.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can comprise a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any amount of inhibiting and/or preventing the growth and/or spread of one or more pathogenic bacteria (e.g., S. pneumoniae) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S can comprise a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any amount of inhibiting and/or preventing the growth and/or spread of one or more pathogenic bacteria (e.g., S. pneumoniae) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S can comprise a 10%
  • pneumoniae infection can comprise a 10-20%, 20-30%, 30-40%, 40-50%, 50-60%, 60-70%, 70-80%, 80-90%, or 90- 100% or any amount of inhibiting and/or preventing the growth and/or spread of one or more pathogenic bacteria (e.g., S. pneumoniae ) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • a pathogenic bacteria e.g., S. pneumoniae
  • a control subject such as, for example, a subject that has not received a disclosed biotherapeutic.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can comprise a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any amount of inhibiting and/or preventing the adherence and/or colonization of one or more pathogenic bacteria (e.g., S. pneumoniae ) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S can comprise a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any amount of inhibiting and/or preventing the adherence and/or colonization of one or more pathogenic bacteria (e.g., S. pneumoniae ) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • pneumoniae infection can comprise a 10-20%, 20-30%, 30-40%, 40-50%, 50-60%, 60-70%, 70-80%, 80-90%, or 90-100% or any amount of inhibiting and/or preventing the adherence and/or colonization of one or more pathogenic bacteria (e.g., S. pneumoniae ) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • pathogenic bacteria e.g., S. pneumoniae
  • a control subject such as, for example, a subject that has not received a disclosed biotherapeutic.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can comprise a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any amount of modulating the endocytosis or paracellular migration of one or more pathogenic bacteria (e.g., S. pneumoniae ) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S can comprise a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any amount of modulating the endocytosis or paracellular migration of one or more pathogenic bacteria (e.g., S. pneumoniae ) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S can comprise a 10%
  • pneumoniae infection can comprise a 10-20%, 20-30%, 30-40%, 40-50%, 50-60%, 60-70%, 70-80%, 80-90%, or 90- 100% or any amount of modulating the endocytosis or paracellular migration of one or more pathogenic bacteria (e.g., S. pneumoniae ) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • pathogenic bacteria e.g., S. pneumoniae
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can comprise a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any amount of inhibiting and/or preventing the spread of one or more pathogenic bacteria (e.g., S. pneumoniae ) by competitive adherence and/or niche occupancy when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • pneumoniae infection can comprise a 10-20%, 20-30%, 30-40%, 40-50%, 50- 60%, 60-70%, 70-80%, 80-90%, or 90-100% or any amount of inhibiting and/or preventing the spread of one or more pathogenic bacteria (e.g., S. pneumoniae) by competitive adherence and/or niche occupancy when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • pathogenic bacteria e.g., S. pneumoniae
  • a control subject such as, for example, a subject that has not received a disclosed biotherapeutic.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can comprise repeating the administering of one or more disclosed biotherapeutics, one or more disclosed secreted factors, a disclosed consortium of probiotics, one or more disclosed probiotics, or any combination thereof.
  • repeating the administering can comprise administering one or more times daily (e.g., 1, 2, 3, or 4 times).
  • repeating the administering can comprise administering on several consecutive days (e.g., for 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 days, or more than 10 days), weeks (e.g., for 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 weeks, or more than 10 weeks), or months (e.g., for 1, 2, 3, 4, 5, or 6 months, or more than 6 months).
  • a disclosed biotherapeutic, a disclosed secreted factor, a disclosed consortium of probiotics, a disclosed probiotic, or any combination thereof can be administered 1 - 3 times per day for about 7 to 21 days.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can comprise monitoring the subject.
  • monitoring the subject can comprise monitoring the subject for the development of adverse effects.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can comprise continuing to treat the subject.
  • continuing to treat the subject can comprise continuing to administer to the subject one or more disclosed biotherapeutics, one or more disclosed secreted factors, a disclosed consortium of probiotics, one or more disclosed probiotics, or any combination thereof.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S in the presence of adverse effects, a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S.
  • modifying one or more steps of a disclosed method can comprise modifying the administering step.
  • modifying the administering step can comprise changing the amount of one or more disclosed biotherapeutics, one or more disclosed secreted factors, a disclosed consortium of probiotics, one or more disclosed probiotics, or any combination thereof administered to the subject, changing the frequency of administration of one or more disclosed biotherapeutics, one or more disclosed secreted factors, a disclosed consortium of probiotics, one or more disclosed probiotics, or any combination thereof, changing the duration of administration of one or more disclosed biotherapeutics, one or more disclosed secreted factors, a disclosed consortium of probiotics, one or more disclosed probiotics, or any combination thereof, changing the route of administration of one or more disclosed biotherapeutics, one or more disclosed secreted factors, a disclosed consortium of probiotics, one or more disclosed probiotics, or any combination thereof, or any combination of disclosed changes.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can comprise manipulating the microbiome to inhibit and/or prevent infection caused by one or more pathogenic bacteria, such as an infection caused by S. pneumoniae.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can comprise manipulating the microbiome to decrease and/or minimize the risk of infection caused by one or more pathogenic bacteria, such as an infection caused by S. pneumoniae.
  • a disclosed method can further comprise administering and/or continuing to administer a therapeutically effective amount of a disclosed biotherapeutic.
  • a disclosed method can further comprise continuing to monitor the subject.
  • the relative abundance of one or more disclosed Corynebacterium sp. when the relative abundance of one or more disclosed Corynebacterium sp. is less than about 50%, about 60%, about 70%, about 80%, or 90% of the microbiome, then the risk of colonization by S. pneumoniae is increased and/or higher and/or enhanced.
  • the relative abundance of one or more disclosed Corynebacterium sp. when the relative abundance of one or more disclosed Corynebacterium sp. is about 50% to about 60%, about 60% to about 70%, about 70% to about 80%, about 80% to about 90% of the microbiome, then the risk of colonization by S. pneumoniae is increased and/or higher and/or enhanced.
  • a disclosed method can further comprise administering and/or continuing to administer a therapeutically effective amount of a disclosed biotherapeutic.
  • a disclosed method can further comprise administering and/or continuing to administer a therapeutically effective amount of a disclosed biotherapeutic.
  • a disclosed method can further comprise administering and/or continuing to administer a therapeutically effective amount of a disclosed biotherapeutic.
  • when the relative abundance of Corynebacterium sp. is less than about 50%, about 60%, about 70%, about 80%, or 90% of the microbiome, then a disclosed method can further comprise administering and/or continuing to administer a therapeutically effective amount of a disclosed biotherapeutic.
  • the relative abundance of Corynebacterium sp. when the relative abundance of Corynebacterium sp.
  • a disclosed method can further comprise continuing to monitor the subject.
  • a disclosed method can further comprise continuing to monitor the subject.
  • a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection can comprise subjecting the subject to one or more invasive or non-invasive diagnostic assessments. Diagnostic assessments are known to the art.
  • a disclosed non-invasive diagnostic assessment can comprise x-rays, computerized tomography (CT) scans, magnetic resonance imaging (MRI) scans, ultrasounds, positron emission tomography (PET) scans, or any combination thereof.
  • a disclosed invasive diagnostic assessment can comprise a tissue biopsy or exploratory surgery.
  • techniques to monitor, measure, and/or assess the restoring one or more aspects of respiratory health can comprise qualitative (or subjective) means as well as quantitative (or objective) means. These means are known to the skilled person. For example, representative regulated variables and sensors relating to systemic homeostasis are discussed supra.
  • a disclosed biotherapeutic, a disclosed secreted factor, a disclosed consortium of probiotics, a disclosed probiotic, or any combination thereof can be administered in the absence of identifying the one or more pathogenic bacteria and/or in the absence of characterizing the microbiome.
  • a disclosed biotherapeutic, a disclosed secreted factor, a disclosed consortium of probiotics, a disclosed probiotic, or any combination thereof can be administered on demand.
  • a disclosed biotherapeutic can be formulated for administration as a pharmaceutical formulation.
  • a disclosed pharmaceutical formulation comprising a probiotic, a consortium of probiotics, factors secreted from a probiotic, factors secreted from a consortium of probiotics, or any combination thereof, and a pharmaceutically acceptable carrier and/or excipient can be used in any disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection.
  • Any pharmaceutical formulation disclosed herein can be used in a disclosed method of reducing the risk of developing a pathogenic bacterial and/or S. pneumoniae infection.
  • Disclosed herein is a method of treating S. pneumoniae colonization and/or infection in a subject, the method comprising administering a therapeutically effective amount of a biotherapeutic to the subject in need thereof, wherein the colonization of S. pneumoniae in the subject’s respiratory system is inhibited and/or prevented following administration.
  • Disclosed herein is a method of treating S. pneumoniae colonization in a subject, the method comprising administering a therapeutically effective amount of a biotherapeutic to the subject in need thereof, thereby inhibiting and/or preventing colonization of S. pneumoniae in the subject’s respiratory system.
  • the colonization and/or infection of S. pneumoniae in the subject’s respiratory system can be inhibited and/or prevented.
  • the spread of colonization and/or the spread infection of S. pneumoniae in the subject’s respiratory system can be inhibited and/or prevented.
  • the risk of developing a S. pneumoniae infection in one or more parts in the subject’s respiratory system can be inhibited and/or prevented.
  • a disclosed method of treating S. pneumoniae colonization and/or infection can further comprise promoting respiratory health in a subject.
  • a disclosed biotherapeutic can inhibit and/or prevent the growth of S. pneumoniae in one or more parts of the subject’s respiratory system.
  • a disclosed method of treating S. pneumoniae colonization and/or infection can further comprise characterizing the microbiome of a biological sample.
  • a disclosed microbiome can comprise the nasopharyngeal microbiome, the nasal microbiome, or both.
  • a disclosed method of treating S. pneumoniae colonization and/or infection can further comprise obtaining a biological sample from the subject.
  • a disclosed biological sample can comprise a nasal swab or lavage, a nasopharyngeal swab or lavage, or a pharyngeal swab or lavage, or any combination thereof.
  • a disclosed biological sample can comprise nasal secretion and/or cough droplets.
  • characterizing the microbiome can comprise (i) collecting a biological sample from the subject; (ii) extracting nucleic acid from the subject’s biological sample; and (iii) sequencing the extracted nucleic acid.
  • sequencing the extracted nucleic acid can generate sequence data.
  • characterizing the microbiome can further comprise analyzing the sequence data using taxonomic classification.
  • using taxonomic classification can comprise PCR amplification.
  • PCR amplification can comprise using primers targeting the 16S rRNA gene.
  • PCR amplification can comprise primers targeting the V4 variable region of the 16S rRNA gene.
  • disclosed primers can comprise a pair of primers.
  • a disclosed pair of primers can comprise a primer having the sequence of SEQ ID NO:01 and a primer having the sequence of SEQ ID NO:02.
  • a disclosed pair of primers can comprise a primer having the sequence of SEQ ID NO: 03 and a primer having the sequence of SEQ ID NO:04.
  • a disclosed pair of primers can comprise a primer having the sequence of SEQ ID NO:05 and a primer having the sequence of SEQ ID NO:06.
  • a disclosed method of treating S. pneumoniae colonization and/or infection can further comprise identifying the one or more pathogenic bacteria.
  • the disclosed pathogenic bacteria can comprise Streptococcus sp.
  • Streptococcus sp. can comprise S. pneumoniae.
  • the disclosed pathogenic bacteria can comprise Staphylococcus sp.
  • Staphylococcus sp. can comprise methicillin-sensitive S. aureus or methicillin- resistant S. aureus.
  • the disclosed pathogenic bacteria can comprise Haemophilus influenzae or Moraxella catarrhalis.
  • a disclosed method of treating S. pneumoniae colonization and/or infection can further comprise diagnosing the subject with an infection.
  • a diagnosed infection can comprise a respiratory infection.
  • a diagnosed infection can affect the subject’s mouth, nose, ears, sinuses, pharynx, trachea, bronchial tubes, lungs, alveoli, bronchioles, capillaries, lung lobes, pleura, cilia, epiglottis, larynx, or any combination thereof.
  • a disclosed method of treating S. pneumoniae colonization and/or infection can further comprise diagnosing the subject with pneumonia, otitis media, sinusitis, rhinosinusitis, or any combination thereof.
  • otitis media can be considered a general term for middle-ear inflammation and can be classified clinically as acute otitis media (AOM), recurrent AOM, OM with effusion (OME), or chronic OME, chronic suppurative OM (CSOM), or middle ear effusion (MEE) (discussed supra).
  • sinusitis can occur when the tissue lining of the sinuses becomes swollen or inflamed.
  • Sinusitis can comprise acute sinusitis (e.g., when symptoms are present for 4 weeks or less), chronic sinusitis (e.g., when the swelling of the sinuses is present for longer than 3 months), or subacute sinusitis (e.g., when the swelling is present between one and three months).
  • rhinosinusitis can occur when the mucosal lining in the paranasal sinuses and nasal cavity becomes inflamed. Most cases of acute rhinosinusitis are caused by viral upper respiratory infections.
  • a disclosed biotherapeutic can comprise a probiotic, a consortium of probiotics, factors secreted from a probiotic, factors secreted from a consortium of probiotics, or any combination thereof.
  • a disclosed biotherapeutic can comprise pharmaceutical formulation comprising a probiotic, a consortium of probiotics, factors secreted from a probiotic, factors secreted from a consortium of probiotics, or any combination thereof, and a pharmaceutically acceptable carrier and/or excipient.
  • a disclosed pharmaceutical formulation can comprise at least one lyoprotectant.
  • a disclosed lyoprotectant can comprise peptone, glycerol, lactose, gelatin, glucose, sucrose, trehalose, dextran, maltodextrin, adonitol, sodium glutamate, or any combination thereof.
  • a disclosed biotherapeutic can be lyophilized or freeze-dried such that, for example, a disclosed probiotic, a disclosed consortium of probiotics, disclosed factors secreted from a probiotic, disclosed factors secreted from a consortium of probiotics, or any combination thereof are all lyophilized or freeze-dried.
  • a disclosed consortium of probiotics can comprise at least one strain from the bacterial genus ( >ryne bacterium , at least one strain from the bacterial genus Dolosigranulum , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus.
  • the at least one strain from the bacterial genus Cory neb acterium can comprise one or more strains of Corynebacterium accolens.
  • the at least one strain from the bacterial genus Dolosigranulum can comprise one or more strains of Dolosigranulum pigrum.
  • the at least one strain from the bacterial genus Streptococcus can comprise one or more strains of Streptococcus mitis, Streptococcus salivarius , Streptococcus oralis , or Streptococcus thermophilus .
  • the at least one strain from the bacterial genus Lactobacillus can comprise one or more strains of Lactobacillus rhamnosus or Lactobacillus acidophilus.
  • a disclosed biotherapeutic can comprises one or more probiotics.
  • one or more disclosed probiotics can comprise at least one strain from the bacterial genus one Corynebacterium sp. In an aspect of a disclosed pharmaceutical formulation, one or more disclosed probiotics can comprise at least one strain from the bacterial genus Corynebacterium and at least one strain from the bacterial genus Dolosigranulum. In an aspect of a disclosed pharmaceutical formulation, one or more disclosed probiotics can comprise at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , and at least one strain from the bacterial genus Streptococcus.
  • one or more disclosed probiotics can comprise at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , and at least one strain from the bacterial genus Lactobacillus. In an aspect of a disclosed pharmaceutical formulation, one or more disclosed probiotics can comprise at least one strain from the bacterial genus Corynebacterium and at least one at least one strain from the bacterial genus Streptococcus.
  • one or more disclosed probiotics can comprise at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus. In an aspect of a disclosed pharmaceutical formulation, one or more probiotics can comprise at least one strain from the bacterial genus Corynebacterium and at least one strain from the bacterial genus Lactobacillus.
  • one or more probiotics can comprise at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus.
  • a disclosed biotherapeutic can comprise one or more factors secreted by a disclosed probiotic or secreted by a disclosed consortium of probiotics.
  • a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus.
  • a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium. In an aspect of a disclosed pharmaceutical formulation, a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium and at least one strain from the bacterial genus Dolosigranulum. In an aspect of a disclosed pharmaceutical formulation, a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , and at least one train from the bacterial genus Streptococcus.
  • a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , and at least one strain from the bacterial genus Lactobacillus.
  • a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium and at least one strain from the bacterial genus Streptococcus.
  • a disclosed biotherapeutic can comprise comprises one or more factors secreted by at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus.
  • a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium and at least one strain from the bacterial genus Lactobacillus.
  • a disclosed Corynebacterium can comprise C. accolens , C. afermentans subsp. afermentans , C.
  • afermentans subsp. lipophilum C. ammoniagenes , C. amycolatum , C. appendicis , C. aquaticum , C. argentoratense , C. atypicum , C. aurimucosum , C. auris, C. bovis, C. canis, C. confusum , C. coyleae , C. diphtheriae , C. durum , C. efficiens , C. equi (now Rhodococcus equi), C. falsenii , C. flavescens , C. grisburgense , C. freneyi , C. glucuronolyticum , C.
  • a disclosed strain from the bacterial genus Corynebacterium can comprise C. accolens , C. coyleae , C. propinquum , C. pseudodiphtheriticum , C. amycolatum , C. glutamicum , C. aurimucosum , C.
  • a disclosed strain from the bacterial genus Corynebacterium can comprise any species identified in Table 13.
  • a disclosed therapeutically effective dose can comprise a total of at least 100 bacterial CFUs of the one or more probiotics, a total of at least 200 to at least 300 bacterial CFUs of the one or more probiotics, a total of at least 300 to at least 400 bacterial CFUs of the one or more probiotics, a total of at least 400 to at least 500 bacterial CFUs of the one or more probiotics, a total of at least 500 to at least 600 bacterial CFUs of the one or more probiotics, a total of at least 600 to at least 700 bacterial CFUs of the one or more probiotics, a total of at least 700 to at least 800 bacterial CFUs of the one or more probiotics, a total of at least 800 to at least 900 bacterial CFUs of the one or more probiotics, a total of at least 900 to at least 1000 bacterial CFUs of the one or more probiotics,
  • a disclosed therapeutically effective dose can comprise a total of at least 1000 to at least 2000 bacterial CFUs of the one or more probiotics, a total of at least 2000 to at least 3000 bacterial CFUs of the one or more probiotics, a total of at least 3000 to at least 4000 bacterial CFUs of the one or more probiotics, a total of at least 4000 to at least 5000 bacterial CFUs of the one or more probiotics, a total of at least 5000 to at least 6000 bacterial CFUs of the one or more probiotics, a total of at least 6000 to at least 7000 bacterial CFUs of the one or more probiotics, a total of at least 8000 to at least 9000 bacterial CFUs of the one or more probiotics, or a total of at least 10,000 bacterial CFUs of one or more disclosed probiotics (such as, for example, Corynebacterium
  • a disclosed therapeutically effective dose can comprise a total of at least 100 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., Lactobacillus sp., or any combination thereof, a total of at least 200 to at least 300 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 300 to at least 400 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 400 to at least 500 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp ., Streptococcus
  • Lactobacillus sp ., or any combination thereof a total of at least 500 to at least 600 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 600 to at least 700 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 700 to at least 800 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 800 to at least 900 bacterial CFUs of Corynebacterium sp .,
  • Lactobacillus sp . or any combination thereof, a total of at least 900 to at least 1000 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, or a total of at least 1000 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof.
  • a disclosed therapeutically effective dose can comprise a total of at least 1000 to at least 2000 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp., Lactobacillus sp., or any combination thereof, a total of at least 2000 to at least 3000 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., Lactobacillus sp., or any combination thereof, a total of at least 3000 to at least 4000 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., Lactobacillus sp., or any combination thereof, a total of at least 4000 to at least 5000 bacterial CFUs of the Corynebacterium sp., Dolosigranulum sp., Strepto
  • Lactobacillus sp., or any combination thereof a total of at least 5000 to at least 6000 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., Lactobacillus sp., or any combination thereof, a total of at least 6000 to at least 7000 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., Lactobacillus sp., or any combination thereof, a total of at least 8000 to at least 9000 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., Lactobacillus sp., or any combination thereof, or a total of at least 10,000 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp., Strepto
  • a disclosed therapeutically effective dose can comprise a total of at least 10 4 to at least 10 5 bacterial CFUs of the one or more probiotics, a total of at least 10 5 to at least 10 6 bacterial CFUs of the one or more probiotics, a total of at least 10 6 to at least 10 7 bacterial CFUs of the one or more probiotics, a total of at least 10 7 to at least 10 8 bacterial CFUs of the one or more probiotics, a total of at least 10 8 to at least 10 9 bacterial CFUs of the one or more probiotics, a total of at least 10 9 to at least 10 10 bacterial CFUs of the one or more probiotics, a total of at least 10 10 to at least 10 11 bacterial CFUs of the one or more probiotics, a total of at least 10 11 to at least 10 12 bacterial CFUs of the one or more probiotics, a total of at least 10 12 bacterial CFUs of the one or more probiotics,
  • a disclosed therapeutically effective dose can comprise at least 10 3 , 10 4 , 10 5 ,
  • a disclosed therapeutically effective dose can comprise Corynebacterium sp., Dolosigranulum sp., Streptococcus sp ., and Lactobacillus sp. in a ratio of about 1 :0.01 :0.01 :0.01 to about 1 : 1 : 1 : 1.
  • a disclosed therapeutically effective dose can comprise Corynebacterium sp ., Dolosigranulum sp., Streptococcus sp., and Lactobacillus sp . in any ratio.
  • adisclosed therapeutically effective dose can comprise a higher dose of Corynebacterium sp., or a higher dose of Dolosigranulum sp., or a higher dose of Streptococcus sp., or a higher dose of Lactobacillus sp. as compared to any other bacteria in the consortium.
  • a disclosed therapeutically effective dose can comprise a dose of Lactobacillus sp. that is about double that of Corynebacterium sp.
  • a disclosed method of treating S. pneumoniae colonization and/or infection can further comprise treating the subject.
  • treating the subject can comprise treating the subject’s respiratory infection.
  • treating the subject can comprise treating the subject’s non-respiratory infection.
  • a disclosed method of treating S. pneumoniae colonization and/or infection can comprise further comprising administering to the subject a therapeutically effective amount of one or more anti -bacterial agents.
  • Anti -bacterial agents and combinations of anti -bacterial agents are known to the art and discussed supra in Part VII(C)(1).
  • a disclosed method of treating S. pneumoniae colonization and/or infection can comprise further comprising administering to the subject a therapeutically effective amount of (i) one or more active agents, (ii) one or more biologically active agents, (iii) one or more pharmaceutically active agents, (iv) one or more immune-based therapeutic agents, (v) one or more clinically approved agents, or (vi) any combination thereof.
  • a therapeutically effective amount of an active agent, a biologically active agent, a pharmaceutically active agent, an immune-based therapeutic active agent, a clinically approved agent, or an anti -bacterial agent can be about 1 ng/kg body weight/day to about 100 ng/kg body weight/day, about 10 ng/kg body weight/day to about 1 pg/kg body, about 100 ng/kg body weight/day to about 10 pg/kg body, about 1 pg/kg body weight/day to about 100 pg/kg body, about 10 pg/kg body weight/day to about 1 mg/kg body, or about 100 pg/kg body weight/day to about 10 mg/kg body.
  • administering a disclosed anti -bacterial agent can comprise systemic or direct administration.
  • administering a disclosed anti -bacterial agent can comprise oral administration, sublingual administration, intravenous administration, intranasal administration, intraperitoneal administration, or any combination thereof.
  • administering a disclosed anti-bacterial agent can be administered by any method of administration disclosed herein.
  • a disclosed anti -bacterial agent can be administered via multiple routes either concurrently or sequentially. A skilled clinician can determine the best route of administration for a disclosed anti -bacterial agent to a subject at a given time.
  • a disclosed anti -bacterial agent can inherently encompass a pharmaceutically acceptable salt thereof.
  • a disclosed method of treating S. pneumoniae colonization and/or infection can further comprise increasing the relative abundance of one or more probiotics in the subject’s microbiome.
  • a disclosed method of treating S. pneumoniae colonization and/or infection can further comprise increasing the relative abundance of one or more of Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., and Lactobacillus sp. in the subject’s microbiome.
  • pneumoniae colonization and/or infection can further comprise increasing the relative abundance of one or more of at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus , or any combination thereof in the subject’s microbiome.
  • a disclosed method of treating S. pneumoniae colonization and/or infection can further comprise increasing the relative abundance of at least one strain from the bacterial genus Corynebacterium in the subject’s microbiome.
  • pneumoniae colonization and/or infection can further comprise increasing the relative abundance of at least one strain from the bacterial genus Dolosigranulum in the subject’s microbiome.
  • a disclosed method of treating S. pneumoniae colonization and/or infection can further comprise increasing the relative abundance of at least one strain from the bacterial genus Streptococcus in the subject’s microbiome.
  • a disclosed method of treating S. pneumoniae colonization and/or infection can further comprise increasing the relative abundance of at least one strain from the bacterial genus Lactobacillus in the subject’s microbiome.
  • a disclosed method of treating S. pneumoniae colonization and/or infection can further comprise decreasing the relative abundance of one or more pathogenic bacteria in the subject’s microbiome. In an aspect, a disclosed method of treating S. pneumoniae colonization and/or infection can further comprise decreasing the relative abundance of S. pneumoniae in the subject’s microbiome. In an aspect, a disclosed method of treating S. pneumoniae colonization and/or infection can further comprise decreasing the relative abundance of a S. aureus in the subject’s microbiome. In an aspect, a disclosed method of treating S. pneumoniae colonization and/or infection can further comprise decreasing the relative abundance of Haemophilus influenzae and/or Moraxella catarrhalis in the subject’s microbiome.
  • a disclosed method of treating S. pneumoniae colonization and/or infection can further comprise administering to the subject one or more therapeutic agents.
  • a disclosed therapeutic agent can comprise a biologically active agent, a pharmaceutically active agent, an anti -bacterial agent, an anti-fungal agent, an anti-viral agent, a corticosteroid, an analgesic, an immunostimulant, an immune-based product, or any combination thereof.
  • administering can comprise intranasal administration, oral administration, sublingual administration, or any combination thereof.
  • a subject in an aspect of a disclosed method of treating S. pneumoniae colonization and/or infection, can be a healthy subject, for example, a subject that does not have an infection and/or is not suspected of having an infection.
  • a subject can be an adult, a child, or an infant. In an aspect, a subject can be a neonate. In an aspect, a subject can be a premature infant. In an aspect, a subject can be immune- compromised. In an aspect, a subject can have diabetes or a chronic disease (e.g., heart disease, kidney disease, or liver disease). In an aspect, a subject can have HIV. In an aspect, a subject can have cancer or has had cancer. In an aspect, a subject can be the recipient of one or more solid organ transplants. In an aspect, a subject can have nephrotic syndrome. In an aspect, a subject can be alcoholic or can smoke cigarettes. In an aspect, a subject can have a chronic lung disease. In an aspect, a disclosed chronic lung disease can comprise emphysema, chronic obstructive lung disease, chronic obstructive pulmonary disease, asthma, or any combination thereof.
  • a chronic lung disease can comprise emphysema, chronic obstructive lung disease
  • a subject can be diagnosed with an infection of one or more parts of the respiratory system. In an aspect, a subject can be suspected of having an infection in one or more parts of the respiratory system. In an aspect, a disclosed therapeutically effective amount of a biotherapeutic can comprise an amount sufficient to inhibit and/or prevent the growth of one or more pathogenic bacteria in one or more parts of the subject’s respiratory system. In an aspect, a disclosed therapeutically effective amount of a biotherapeutic can comprise an amount sufficient to inhibit and/or prevent the spread of one or more pathogenic bacteria from a first part of the subject’s respiratory system to a second part of the subject’s respiratory system.
  • one or more disclosed probiotics can inhibit and/or prevent the growth and/or spread of one or more pathogenic bacteria using competitive adherence and/or non-adherence mechanisms (e.g., secretion of antimicrobial factors). In an aspect, one or more disclosed probiotics can inhibit and/or prevent the adherence and/or colonization of one or more pathogenic bacteria. In an aspect, one or more disclosed probiotics can modulate the endocytosis or paracellular migration of one or more pathogenic bacteria. In an aspect, one or more disclosed probiotics can inhibit and/or prevent the spread of one or more pathogenic bacteria by competitive adherence and/or niche occupancy.
  • one or more disclosed probiotics can inhibit and/or prevent the growth and/or spread of S. pneumoniae using competitive adherence and/or non-adherence mechanisms (e.g., secretion of antimicrobial factors). In an aspect, one or more disclosed probiotics can inhibit and/or prevent the adherence and/or colonization of S. pneumoniae. In an aspect, one or more disclosed probiotics can modulate the endocytosis or paracellular migration of S. pneumoniae. In an aspect, one or more disclosed probiotics can inhibit and/or prevent the spread S. pneumoniae by competitive adherence and/or niche occupancy.
  • one or more disclosed probiotics can secrete one or more factors.
  • a disclosed secreted factor can be species-dependent and/or strain-dependent.
  • a disclosed secreted factor can inhibit and/or prevent the growth and/or spread of one or more pathogenic bacteria.
  • a disclosed secreted factor can inhibit and/or prevent the adherence and/or colonization of one or more pathogenic bacteria.
  • a disclosed secreted factor can modulate the endocytosis or paracellular migration of one or more pathogenic bacteria.
  • a disclosed secreted factor can inhibit and/or prevent the spread of one or more pathogenic bacteria by competitive adherence and/or niche occupancy.
  • a disclosed secreted factor can inhibit and/or prevent the growth and/or spread of S. pneumoniae.
  • a disclosed secreted factor can inhibit and/or prevent the adherence and/or colonization of S. pneumoniae.
  • a disclosed secreted factor can modulate the endocytosis or paracellular migration of S. pneumoniae.
  • a disclosed secreted factor can inhibit and/or prevent the spread of S. pneumoniae by competitive adherence and/or niche occupancy.
  • Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., Lactobacillus sp., or any combination thereof can secrete one or more factors that inhibit and/or prevent the growth and/or spread of one or more pathogenic bacteria.
  • Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., Lactobacillus sp. can secrete one or more factors that inhibit and/or prevent the growth and/or spread of one or more pathogenic bacteria.
  • pneumoniae colonization and/or infection Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof can secrete one or more factors that inhibit and/or prevent the adherence and/or colonization of one or more pathogenic bacteria.
  • Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., Lactobacillus sp., or any combination thereof can secrete one or more secreted factors that modulate the endocytosis or paracellular migration of one or more pathogenic bacteria.
  • Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof can secrete one or more secreted factors inhibit and/or prevent the spread of one or more pathogenic bacteria by competitive adherence and/or niche occupancy.
  • S. pneumoniae colonization and/or infection Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof can secrete one or more secreted factors inhibit and/or prevent the spread of one or more pathogenic bacteria by competitive adherence and/or niche occupancy.
  • Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof can secrete one or more secreted factors inhibit and/or prevent the growth and/or spread of S. pneumoniae.
  • Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof can secrete one or more factors inhibit and/or prevent the adherence and/or colonization of S. pneumoniae.
  • a disclosed method of treating S. pneumoniae colonization and/or infection, Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof secrete one or more factors can modulate the endocytosis or paracellular migration of S. pneumoniae.
  • Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof can secrete one or more factors inhibit and/or prevent the spread of S. pneumoniae by competitive adherence and/or niche occupancy.
  • Corynebacterium sp. can secrete one or more factors that inhibit and/or prevent the growth and/or spread of one or more pathogenic bacteria. In an aspect of a disclosed method of treating S. pneumoniae colonization and/or infection, Corynebacterium sp. can secrete one or more factors that inhibit and/or prevent the adherence and/or colonization of one or more pathogenic bacteria. In an aspect of a disclosed method of treating S. pneumoniae colonization and/or infection, Corynebacterium sp. can secrete one or more secreted factors that modulate the endocytosis or paracellular migration of one or more pathogenic bacteria.
  • Corynebacterium sp. can secrete one or more secreted factors that inhibit and/or prevent the spread of one or more pathogenic bacteria by competitive adherence and/or niche occupancy.
  • Corynebacterium sp. can secrete one or more secreted factors that inhibit and/or prevent the growth and/or spread of S. pneumoniae. In an aspect of a disclosed method of treating S. pneumoniae colonization and/or infection, Corynebacterium sp. can secrete one or more factors that inhibit and/or prevent the adherence and/or colonization of S. pneumoniae. In an aspect of a disclosed method of treating S. pneumoniae colonization and/or infection, Corynebacterium sp. can secrete one or more factors that modulate the endocytosis or paracellular migration of S. pneumoniae. In an aspect of a disclosed method of treating S. pneumoniae colonization and/or infection, Corynebacterium sp. can secrete one or more factors that inhibit and/or prevent the spread of S. pneumoniae by competitive adherence and/or niche occupancy.
  • a disclosed method of treating S. pneumoniae colonization and/or infection can comprise a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any amount of inhibiting and/or preventing the growth and/or spread of one or more pathogenic bacteria (e.g., S. pneumoniae) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • pneumoniae colonization and/or infection can comprise a 10-20%, 20-30%, 30-40%, 40-50%, 50-60%, 60- 70%, 70-80%, 80-90%, or 90-100% or any amount of inhibiting and/or preventing the growth and/or spread of one or more pathogenic bacteria (e.g., S. pneumoniae) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • a disclosed method of treating S can comprise a 10-20%, 20-30%, 30-40%, 40-50%, 50-60%, 60- 70%, 70-80%, 80-90%, or 90-100% or any amount of inhibiting and/or preventing the growth and/or spread of one or more pathogenic bacteria (e.g., S. pneumoniae) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • pneumoniae colonization and/or infection can comprise a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any amount of inhibiting and/or preventing the adherence and/or colonization of one or more pathogenic bacteria (e.g., S. pneumoniae) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • a disclosed method of treating S can comprise a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any amount of inhibiting and/or preventing the adherence and/or colonization of one or more pathogenic bacteria (e.g., S. pneumoniae) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • a disclosed method of treating S can comprise a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any amount of inhibiting and/or preventing the adherence and/or colonization of one
  • pneumoniae colonization and/or infection can comprise a 10-20%, 20-30%, 30-40%, 40-50%, 50- 60%, 60-70%, 70-80%, 80-90%, or 90-100% or any amount of inhibiting and/or preventing the adherence and/or colonization of one or more pathogenic bacteria (e.g., S. pneumoniae) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • pathogenic bacteria e.g., S. pneumoniae
  • a disclosed method of treating S. pneumoniae colonization and/or infection can comprise a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any amount of modulating the endocytosis or paracellular migration of one or more pathogenic bacteria (e.g., S. pneumoniae) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • pneumoniae colonization and/or infection can comprise a 10-20%, 20-30%, 30-40%, 40-50%, 50-60%, 60- 70%, 70-80%, 80-90%, or 90-100% or any amount of modulating the endocytosis or paracellular migration of one or more pathogenic bacteria (e.g., S. pneumoniae ) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • pathogenic bacteria e.g., S. pneumoniae
  • a disclosed method of treating S. pneumoniae colonization and/or infection can comprise a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any amount of inhibiting and/or preventing the spread of one or more pathogenic bacteria (e.g., S. pneumoniae ) by competitive adherence and/or niche occupancy when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • pneumoniae colonization and/or infection can comprise a 10-20%, 20-30%, 30-40%, 40-50%, 50-60%, 60-70%, 70-80%, 80-90%, or 90-100% or any amount of inhibiting and/or preventing the spread of one or more pathogenic bacteria (e.g., S. pneumoniae ) by competitive adherence and/or niche occupancy when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • pathogenic bacteria e.g., S. pneumoniae
  • a control subject such as, for example, a subject that has not received a disclosed biotherapeutic
  • a disclosed method of treating S. pneumoniae colonization and/or infection can comprise repeating the administering of one or more disclosed biotherapeutics, one or more disclosed secreted factors, a disclosed consortium of probiotics, one or more disclosed probiotics, or any combination thereof.
  • repeating the administering can comprise administering one or more times daily (e.g., 1, 2, 3, or 4 times).
  • repeating the administering can comprise administering on several consecutive days (e.g., for 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 days, or more than 10 days), weeks (e.g., for 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 weeks, or more than 10 weeks), or months (e.g., for 1, 2, 3, 4, 5, or 6 months, or more than 6 months).
  • a disclosed biotherapeutic, a disclosed secreted factor, a disclosed consortium of probiotics, a disclosed probiotic, or any combination thereof can be administered 1 - 3 times per day for about 7 to 21 days.
  • a disclosed method of treating S. pneumoniae colonization and/or infection can comprise monitoring the subject.
  • monitoring the subject can comprise monitoring the subject for the development of adverse effects.
  • a disclosed method of treating S. pneumoniae colonization and/or infection can comprise continuing to treat the subject.
  • continuing to treat the subject can comprise continuing to administer to the subject one or more disclosed biotherapeutics, one or more disclosed secreted factors, a disclosed consortium of probiotics, one or more disclosed probiotics, or any combination thereof.
  • a disclosed method of treating S. pneumoniae colonization and/or infection can comprise modifying one or more steps of the method.
  • modifying one or more steps of a disclosed method can comprise modifying the administering step.
  • modifying the administering step can comprise changing the amount of one or more disclosed biotherapeutics, one or more disclosed secreted factors, a disclosed consortium of probiotics, one or more disclosed probiotics, or any combination thereof administered to the subject, changing the frequency of administration of one or more disclosed biotherapeutics, one or more disclosed secreted factors, a disclosed consortium of probiotics, one or more disclosed probiotics, or any combination thereof, changing the duration of administration of one or more disclosed biotherapeutics, one or more disclosed secreted factors, a disclosed consortium of probiotics, one or more disclosed probiotics, or any combination thereof, changing the route of administration of one or more disclosed biotherapeutics, one or more disclosed secreted factors, a disclosed consortium of probiotics, one or more disclosed probiotics, or any combination thereof, or any combination of disclosed changes.
  • a disclosed method of treating S. pneumoniae colonization and/or infection can comprise manipulating the microbiome to inhibit and/or prevent infection caused by one or more pathogenic bacteria, such as an infection caused by S. pneumoniae.
  • a disclosed method of treating S. pneumoniae colonization and/or infection can comprise manipulating the microbiome to decrease and/or minimize the risk of infection caused by one or more pathogenic bacteria, such as an infection caused by S. pneumoniae. For example, in an aspect, when the relative abundance of one or more disclosed Corynebacterium sp. is below a threshold level of 1.2 x 10 6 16S rRNA gene copies per biological sample, then the risk of colonization by S. pneumoniae is increased and/or higher and/or enhanced.
  • a disclosed method can further comprise administering and/or continuing to administer a therapeutically effective amount of a disclosed biotherapeutic.
  • a disclosed method can further comprise continuing to monitor the subject.
  • a disclosed method of promoting respiratory health can comprise manipulating the microbiome to inhibit and/or prevent infection caused by one or more pathogenic bacteria, such as an infection caused by S. pneumoniae.
  • a disclosed method of promoting respiratory health can comprise manipulating the microbiome to decrease and/or minimize the risk of infection caused by one or more pathogenic bacteria, such as an infection caused by S. pneumoniae. For example, in an aspect, when the relative abundance of one or more disclosed Corynebacterium sp. is below a threshold level of 1.2 x 10 6 16S rRNA gene copies per biological sample, then the risk of colonization by S. pneumoniae is increased and/or higher and/or enhanced.
  • a disclosed method can further comprise administering and/or continuing to administer a therapeutically effective amount of a disclosed biotherapeutic.
  • a disclosed method can further comprise continuing to monitor the subject.
  • the relative abundance of one or more disclosed Corynebacterium sp. when the relative abundance of one or more disclosed Corynebacterium sp. is less than about 50%, about 60%, about 70%, about 80%, or 90% of the microbiome, then the risk of colonization by S. pneumoniae is increased and/or higher and/or enhanced.
  • the relative abundance of one or more disclosed Corynebacterium sp. when the relative abundance of one or more disclosed Corynebacterium sp. is about 50% to about 60%, about 60% to about 70%, about 70% to about 80%, about 80% to about 90% of the microbiome, then the risk of colonization by S. pneumoniae is increased and/or higher and/or enhanced.
  • a disclosed method can further comprise administering and/or continuing to administer a therapeutically effective amount of a disclosed biotherapeutic.
  • a disclosed method can further comprise administering and/or continuing to administer a therapeutically effective amount of a disclosed biotherapeutic.
  • a disclosed method can further comprise administering and/or continuing to administer a therapeutically effective amount of a disclosed biotherapeutic.
  • when the relative abundance of Corynebacterium sp. is less than about 50%, about 60%, about 70%, about 80%, or 90% of the microbiome, then a disclosed method can further comprise administering and/or continuing to administer a therapeutically effective amount of a disclosed biotherapeutic.
  • the relative abundance of Corynebacterium sp. when the relative abundance of Corynebacterium sp.
  • a disclosed method can further comprise continuing to monitor the subject.
  • a disclosed method can further comprise continuing to monitor the subject.
  • a disclosed method of treating S. pneumoniae colonization and/or infection can comprise subjecting the subject to one or more invasive or non-invasive diagnostic assessments. Diagnostic assessments are known to the art.
  • a disclosed non-invasive diagnostic assessment can comprise x-rays, computerized tomography (CT) scans, magnetic resonance imaging (MRI) scans, ultrasounds, positron emission tomography (PET) scans, or any combination thereof.
  • a disclosed invasive diagnostic assessment can comprise a tissue biopsy or exploratory surgery.
  • techniques to monitor, measure, and/or assess the restoring one or more aspects of respiratory health can comprise qualitative (or subjective) means as well as quantitative (or objective) means. These means are known to the skilled person. For example, representative regulated variables and sensors relating to systemic homeostasis are discussed supra.
  • a disclosed biotherapeutic, a disclosed secreted factor, a disclosed consortium of probiotics, a disclosed probiotic, or any combination thereof can be administered in the absence of identifying the one or more pathogenic bacteria and/or in the absence of characterizing the microbiome.
  • a disclosed biotherapeutic, a disclosed secreted factor, a disclosed consortium of probiotics, a disclosed probiotic, or any combination thereof can be administered on demand.
  • a disclosed biotherapeutic can be formulated for administration as a pharmaceutical formulation.
  • a disclosed pharmaceutical formulation comprising a probiotic, a consortium of probiotics, factors secreted from a probiotic, factors secreted from a consortium of probiotics, or any combination thereof, and a pharmaceutically acceptable carrier and/or excipient can be used in any disclosed method of treating S. pneumoniae colonization and/or infection.
  • Any pharmaceutical formulation disclosed herein can be used in a disclosed method of treating S. pneumoniae colonization and/or infection.
  • a method of modulating microbial diversity and/or composition in a subject comprising characterizing the microbiome of a biological sample obtained from a subject; and administering one or more biotherapeutics to the subject, wherein following administration, the microbiome is modulated.
  • a subject in an aspect of a disclosed method of modulating microbial diversity and/or composition, can be any subject. In an aspect, a subject that does not have an infection and/or is not suspected of having an infection.
  • a disclosed microbiome can comprise the nasopharyngeal microbiome, the nasal microbiome, or both.
  • a disclosed method of modulating microbial diversity and/or composition can further comprise reducing the subject’s risk of developing a pathogenic bacterial infection.
  • a disclosed method of modulating microbial diversity and/or composition can further comprise preventing and/or inhibiting the colonization of a pathogenic bacteria in the subject’s respiratory system.
  • a disclosed method of modulating microbial diversity and/or composition can further comprise preventing and/or inhibiting the colonization of S. pneumoniae in the subject’s respiratory system.
  • a disclosed method of modulating microbial diversity and/or composition following administration, the colonization of a pathogenic bacteria and/or S. pneumoniae in the subject’s respiratory system can be inhibited and/or prevented.
  • a disclosed method of modulating microbial diversity and/or composition can further comprise promoting respiratory health in a subject.
  • a disclosed biotherapeutic can inhibit and/or prevent the growth of one or more pathogenic bacteria and/or S. pneumoniae in one or more parts of the subject’s respiratory system.
  • a disclosed method of modulating microbial diversity and/or composition can further comprise obtaining a biological sample from the subject.
  • a disclosed biological sample can comprise a nasal swab or lavage, a nasopharyngeal swab or lavage, or a pharyngeal swab or lavage, or any combination thereof.
  • a disclosed biological sample can comprise nasal secretion and/or cough droplets.
  • characterizing the microbiome can comprise (i) collecting a biological sample from the subject; (ii) extracting nucleic acid from the subject’s biological sample; and (iii) sequencing the extracted nucleic acid.
  • sequencing the extracted nucleic acid can generate sequence data.
  • characterizing the microbiome can further comprise analyzing the sequence data using taxonomic classification.
  • using taxonomic classification can comprise PCR amplification.
  • PCR amplification can comprise using primers targeting the 16S rRNA gene.
  • PCR amplification can comprise primers targeting the V4 variable region of the 16S rRNA gene.
  • disclosed primers can comprise a pair of primers.
  • a disclosed pair of primers can comprise a primer having the sequence of SEQ ID NO:01 and a primer having the sequence of SEQ ID NO:02.
  • a disclosed pair of primers can comprise a primer having the sequence of SEQ ID NO: 03 and a primer having the sequence of SEQ ID NO:04.
  • a disclosed pair of primers can comprise a primer having the sequence of SEQ ID NO:05 and a primer having the sequence of SEQ ID NO:06.
  • a disclosed method of modulating microbial diversity and/or composition can further comprise identifying the one or more pathogenic bacteria.
  • the disclosed pathogenic bacteria can comprise Streptococcus sp.
  • Streptococcus sp. can comprise S. pneumoniae.
  • the disclosed pathogenic bacteria can comprise Staphylococcus sp.
  • Staphylococcus sp. can comprise methicillin-sensitive S. aureus or methicillin- resistant S. aureus.
  • the disclosed pathogenic bacteria can comprise Haemophilus influenzae or Moraxella catarrhalis.
  • a disclosed method of modulating microbial diversity and/or composition can further comprise diagnosing the subject with an infection.
  • a diagnosed infection can comprise a respiratory infection.
  • a diagnosed infection can affect the subject’s mouth, nose, ears, sinuses, pharynx, trachea, bronchial tubes, lungs, alveoli, bronchioles, capillaries, lung lobes, pleura, cilia, epiglottis, larynx, or any combination thereof.
  • a disclosed method of modulating microbial diversity and/or composition can further comprise diagnosing the subject with pneumonia, otitis media, sinusitis, rhinosinusitis, or any combination thereof.
  • otitis media can be considered a general term for middle-ear inflammation and can be classified clinically as acute otitis media (AOM), recurrent AOM, OM with effusion (OME), or chronic OME, chronic suppurative OM (CSOM), or middle ear effusion (MEE) (discussed supra).
  • sinusitis can occur when the tissue lining of the sinuses becomes swollen or inflamed.
  • Sinusitis can comprise acute sinusitis (e.g., when symptoms are present for 4 weeks or less), chronic sinusitis (e.g., when the swelling of the sinuses is present for longer than 3 months), or subacute sinusitis (e.g., when the swelling is present between one and three months).
  • rhinosinusitis can occur when the mucosal lining in the paranasal sinuses and nasal cavity becomes inflamed. Most cases of acute rhinosinusitis are caused by viral upper respiratory infections.
  • a disclosed biotherapeutic can comprise a probiotic, a consortium of probiotics, factors secreted from a probiotic, factors secreted from a consortium of probiotics, or any combination thereof.
  • a disclosed biotherapeutic can comprise pharmaceutical formulation comprising a probiotic, a consortium of probiotics, factors secreted from a probiotic, factors secreted from a consortium of probiotics, or any combination thereof, and a pharmaceutically acceptable carrier and/or excipient.
  • a disclosed pharmaceutical formulation can comprise at least one lyoprotectant.
  • a disclosed lyoprotectant can comprise peptone, glycerol, lactose, gelatin, glucose, sucrose, trehalose, dextran, maltodextrin, adonitol, sodium glutamate, or any combination thereof.
  • a disclosed biotherapeutic can be lyophilized or freeze-dried such that, for example, a disclosed probiotic, a disclosed consortium of probiotics, disclosed factors secreted from a probiotic, disclosed factors secreted from a consortium of probiotics, or any combination thereof are all lyophilized or freeze-dried.
  • a disclosed consortium of probiotics can comprise at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus.
  • a disclosed biotherapeutic can comprises one or more probiotics.
  • the at least one strain from the bacterial genus Cory neb acterium can comprise one or more strains of Corynebacterium accolens.
  • the at least one strain from the bacterial genus Dolosigranulum can comprise one or more strains of Dolosigranulum pigrum.
  • the at least one strain from the bacterial genus Streptococcus can comprise one or more strains of Streptococcus mitis, Streptococcus salivarius , Streptococcus oralis , or Streptococcus thermophilus .
  • the at least one strain from the bacterial genus Lactobacillus can comprise one or more strains of Lactobacillus rhamnosus or Lactobacillus acidophilus.
  • one or more disclosed probiotics can comprise at least one strain from the bacterial genus one Corynebacterium sp. In an aspect of a disclosed pharmaceutical formulation, one or more disclosed probiotics can comprise at least one strain from the bacterial genus Corynebacterium and at least one strain from the bacterial genus Dolosigranulum. In an aspect of a disclosed pharmaceutical formulation, one or more disclosed probiotics can comprise at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , and at least one strain from the bacterial genus Streptococcus.
  • one or more disclosed probiotics can comprise at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , and at least one strain from the bacterial genus Lactobacillus. In an aspect of a disclosed pharmaceutical formulation, one or more disclosed probiotics can comprise at least one strain from the bacterial genus Corynebacterium and at least one at least one strain from the bacterial genus Streptococcus.
  • one or more disclosed probiotics can comprise at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus. In an aspect of a disclosed pharmaceutical formulation, one or more probiotics can comprise at least one strain from the bacterial genus Corynebacterium and at least one strain from the bacterial genus Lactobacillus.
  • one or more probiotics can comprise at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus.
  • a disclosed biotherapeutic can comprise one or more factors secreted by a disclosed probiotic or secreted by a disclosed consortium of probiotics.
  • a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium, at least one strain from the bacterial genus Dolosigranulum , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus.
  • a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium.
  • a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium and at least one strain from the bacterial genus Dolosigranulum. In an aspect, a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , and at least one train from the bacterial genus Streptococcus.
  • a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , and at least one strain from the bacterial genus Lactobacillus. In an aspect, a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium and at least one strain from the bacterial genus Streptococcus.
  • a disclosed biotherapeutic can comprise comprises one or more factors secreted by at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus.
  • a disclosed biotherapeutic can comprise one or more factors secreted by at least one strain from the bacterial genus Corynebacterium and at least one strain from the bacterial genus Lactobacillus.
  • a disclosed Corynebacterium can comprise C. accolens , C. afermentans subsp. afermentans , C. afermentans subsp.
  • a disclosed strain from the bacterial genus Corynebacterium can comprise C. accolens , C. coyleae , C. propinquum , C. pseudodiphtheriticum , C. amycolatum , C. glutamicum , C. aurimucosum , C.
  • a disclosed strain from the bacterial genus Corynebacterium can comprise any species identified in Table 13.
  • a disclosed therapeutically effective dose can comprise a total of at least 100 bacterial CFUs of the one or more probiotics, a total of at least 200 to at least 300 bacterial CFUs of the one or more probiotics, a total of at least 300 to at least 400 bacterial CFUs of the one or more probiotics, a total of at least 400 to at least 500 bacterial CFUs of the one or more probiotics, a total of at least 500 to at least 600 bacterial CFUs of the one or more probiotics, a total of at least 600 to at least 700 bacterial CFUs of the one or more probiotics, a total of at least 700 to at least 800 bacterial CFUs of the one or more probiotics, a total of at least 800 to at least 900 bacterial CFUs of the one or more probiotics, a total of at least 900 to at least 1000 bacterial CFUs of the one or more probiotics,
  • a disclosed therapeutically effective dose can comprise a total of at least 1000 to at least 2000 bacterial CFUs of the one or more probiotics, a total of at least 2000 to at least 3000 bacterial CFUs of the one or more probiotics, a total of at least 3000 to at least 4000 bacterial CFUs of the one or more probiotics, a total of at least 4000 to at least 5000 bacterial CFUs of the one or more probiotics, a total of at least 5000 to at least 6000 bacterial CFUs of the one or more probiotics, a total of at least 6000 to at least 7000 bacterial CFUs of the one or more probiotics, a total of at least 8000 to at least 9000 bacterial CFUs of the one or more probiotics, or a total of at least 10,000 bacterial CFUs of one or more disclosed probiotics (such as, for example, Corynebacterium s
  • a disclosed therapeutically effective dose can comprise a total of at least 100 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., Lactobacillus sp., or any combination thereof, a total of at least 200 to at least 300 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., Lactobacillus sp., or any combination thereof, a total of at least 300 to at least 400 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 400 to at least 500 bacterial CFUs of Corynebacterium sp.
  • Lactobacillus sp ., or any combination thereof a total of at least 500 to at least 600 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 600 to at least 700 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 700 to at least 800 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, a total of at least 800 to at least 900 bacterial CFUs of Corynebacterium sp .,
  • Lactobacillus sp . or any combination thereof, a total of at least 900 to at least 1000 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof, or a total of at least 1000 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof.
  • a disclosed therapeutically effective dose can comprise a total of at least 1000 to at least 2000 bacterial CFUs of Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp., Lactobacillus sp., or any combination thereof, a total of at least 2000 to at least 3000 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., Lactobacillus sp., or any combination thereof, a total of at least 3000 to at least 4000 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., Lactobacillus sp., or any combination thereof, a total of at least 4000 to at least 5000 bacterial CFUs of the Corynebacterium sp., Dolosigranulum sp., Strepto
  • Lactobacillus sp., or any combination thereof a total of at least 5000 to at least 6000 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., Lactobacillus sp., or any combination thereof, a total of at least 6000 to at least 7000 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., Lactobacillus sp., or any combination thereof, a total of at least 8000 to at least 9000 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., Lactobacillus sp., or any combination thereof, or a total of at least 10,000 bacterial CFUs of Corynebacterium sp., Dolosigranulum sp., Strepto
  • a disclosed therapeutically effective dose can comprise a total of at least 10 4 to at least 10 5 bacterial CFUs of the one or more probiotics, a total of at least 10 5 to at least 10 6 bacterial CFUs of the one or more probiotics, a total of at least 10 6 to at least 10 7 bacterial CFUs of the one or more probiotics, a total of at least 10 7 to at least 10 8 bacterial CFUs of the one or more probiotics, a total of at least 10 8 to at least 10 9 bacterial CFUs of the one or more probiotics, a total of at least 10 9 to at least 10 10 bacterial CFUs of the one or more probiotics, a total of at least 10 10 to at least 10 11 bacterial CFUs of the one or more probiotics, a total of at least 10 11 to at least 10 12 bacterial CFUs of the one or more probiotics, a total of at least 10 12 bacterial CFUs of the one or more probiotics,
  • a disclosed therapeutically effective dose can comprise at least 10 3 , 10 4 , 10 5 ,
  • a disclosed therapeutically effective dose can comprise any amount or an unlimited amount of bacterial CFUs of the one or more probiotics.
  • a disclosed therapeutically effective dose can comprise Corynebacterium sp., Dolosigranulum sp., Streptococcus sp ., and Lactobacillus sp. in a ratio of about 1 :0.01 :0.01 :0.01 to about 1 : 1 : 1 : 1.
  • a disclosed therapeutically effective dose can comprise Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., and Lactobacillus sp. in a ratio of about 1:0.01:0.01:0.01 to about 1 : 1 : 1 : 1.
  • a disclosed therapeutically effective dose can comprise Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., and Lactobacillus sp. in any ratio.
  • a disclosed therapeutically effective dose can comprise a higher dose of Corynebacterium sp ., or a higher dose of Dolosigranulum sp ., or a higher dose of Streptococcus sp ., or a higher dose of Lactobacillus sp. as compared to any other bacteria in the consortium.
  • a disclosed therapeutically effective dose can comprise a dose of Lactobacillus sp. that is about double that of Corynebacterium sp.
  • a disclosed method of modulating microbial diversity and/or composition can further comprise treating the subject.
  • treating the subject can comprise treating the subject’s respiratory infection.
  • treating the subject can comprise treating the subject’s non-respiratory infection.
  • a disclosed method of modulating microbial diversity and/or composition can comprise further comprising administering to the subject a therapeutically effective amount of one or more anti -bacterial agents.
  • Anti -bacterial agents and combinations of anti -bacterial agents are known to the art and discussed supra in Part VII(C)(1).
  • a therapeutically effective amount of a disclosed anti -bacterial agent can comprise a dose of about 1 ng/kg body weight/day to about 100 ng/kg body weight/day, about 10 ng/kg body weight/day to about 1 pg/kg body, about 100 ng/kg body weight/day to about 10 pg/kg body, about 1 pg/kg body weight/day to about 100 pg/kg body, about 10 pg/kg body weight/day to about 1 mg/kg body, or about 100 pg/kg body weight/day to about 10 mg/kg body.
  • a disclosed method of modulating microbial diversity and/or composition can comprise further administering to the subject a therapeutically effective amount of (i) one or more active agents, (ii) one or more biologically active agents, (iii) one or more pharmaceutically active agents, (iv) one or more immune-based therapeutic agents, (v) one or more clinically approved agents, or (vi) any combination thereof.
  • a therapeutically effective amount of an active agent, a biologically active agent, a pharmaceutically active agent, an immune-based therapeutic active agent, a clinically approved agent, or an anti -bacterial agent can be about 1 ng/kg body weight/day to about 100 ng/kg body weight/day, about 10 ng/kg body weight/day to about 1 m /1 ⁇ body, about 100 ng/kg body weight/day to about 10 pg/kg body, about 1 pg/kg body weight/day to about 100 pg/kg body, about 10 pg/kg body weight/day to about 1 mg/kg body, or about 100 pg/kg body weight/day to about 10 mg/kg body.
  • administering a disclosed anti -bacterial agent can comprise systemic or direct administration.
  • administering a disclosed anti -bacterial agent can comprise oral administration, sublingual administration, intravenous administration, intranasal administration, intraperitoneal administration, or any combination thereof.
  • administering a disclosed anti -bacterial agent can be administered by any method of administration disclosed herein.
  • a disclosed anti -bacterial agent can be administered via multiple routes either concurrently or sequentially. A skilled clinician can determine the best route of administration for a disclosed anti -bacterial agent to a subject at a given time.
  • a disclosed anti -bacterial agent can inherently encompass a pharmaceutically acceptable salt thereof.
  • disclosed method of modulating microbial diversity and/or composition can further comprise increasing the relative abundance of one or more probiotics in the subject’s microbiome.
  • disclosed method of modulating microbial diversity and/or composition can further comprise increasing the relative abundance of one or more of Corynebacterium sp., Dolosigranulum sp ., Streptococcus sp ., and Lactobacillus sp. in the subject’s microbiome.
  • disclosed method of modulating microbial diversity and/or composition can further comprise increasing the relative abundance of one or more of at least one strain from the bacterial genus Corynebacterium , at least one strain from the bacterial genus Dolosigranulum , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus , or any combination thereof in the subject’s microbiome.
  • disclosed method of modulating microbial diversity and/or composition can further comprise increasing the relative abundance of at least one strain from the bacterial genus Corynebacterium in the subject’s microbiome.
  • disclosed method of modulating microbial diversity and/or composition can further comprise increasing the relative abundance of at least one strain from the bacterial genus Dolosigranulum in the subject’s microbiome. In an aspect, disclosed method of modulating microbial diversity and/or composition can further comprise increasing the relative abundance of at least one strain from the bacterial genus Streptococcus in the subject’s microbiome. In an aspect, disclosed method of modulating microbial diversity and/or composition can further comprise increasing the relative abundance of at least one strain from the bacterial genus Lactobacillus in the subject’s microbiome.
  • a disclosed method of modulating microbial diversity and/or composition can further comprise decreasing the relative abundance of one or more pathogenic bacteria in the subject’s microbiome. In an aspect, a disclosed method of modulating microbial diversity and/or composition can further comprise decreasing the relative abundance of S. pneumoniae in the subject’s microbiome. In an aspect, a disclosed method of modulating microbial diversity and/or composition can further comprise decreasing the relative abundance of a S. aureus in the subject’s microbiome. In an aspect, a disclosed method of modulating microbial diversity and/or composition can further comprise decreasing the relative abundance of Haemophilus influenzae and/or Moraxella catarrhalis in the subject’s microbiome.
  • a disclosed method of modulating microbial diversity and/or composition can further comprise administering to the subject one or more therapeutic agents.
  • a disclosed therapeutic agent can comprise a biologically active agent, a pharmaceutically active agent, an anti -bacterial agent, an anti-fungal agent, an anti-viral agent, a corticosteroid, an analgesic, an immunostimulant, an immune-based product, or any combination thereof.
  • administering can comprise intranasal administration, oral administration, sublingual administration, or any combination thereof.
  • a subject in an aspect of a disclosed method of modulating microbial diversity and/or composition, can be a healthy subject, for example, a subject that does not have an infection and/or is not suspected of having an infection.
  • a subject can be an adult, a child, or an infant. In an aspect, a subject can be a neonate. In an aspect, a subject can be a premature infant. In an aspect, a subject can be immune- compromised. In an aspect, a subject can have diabetes or a chronic disease (e.g., heart disease, kidney disease, or liver disease). In an aspect, a subject can have HIV. In an aspect, a subject can have cancer or has had cancer. In an aspect, a subject can be the recipient of one or more solid organ transplants. In an aspect, a subject can have nephrotic syndrome. In an aspect, a subject can be alcoholic or can smoke cigarettes. In an aspect, a subject can have a chronic lung disease. In an aspect, a disclosed chronic lung disease can comprise emphysema, chronic obstructive lung disease, chronic obstructive pulmonary disease, asthma, or any combination thereof.
  • a chronic lung disease can comprise emphysema, chronic obstructive lung disease
  • a subject can be diagnosed with an infection of one or more parts of the respiratory system. In an aspect, a subject can be suspected of having an infection in one or more parts of the respiratory system. In an aspect, a disclosed therapeutically effective amount of a biotherapeutic can comprise an amount sufficient to inhibit and/or prevent the growth of one or more pathogenic bacteria in one or more parts of the subject’s respiratory system. In an aspect, a disclosed therapeutically effective amount of a biotherapeutic can comprise an amount sufficient to inhibit and/or prevent the spread of one or more pathogenic bacteria from a first part of subj ec s respiratory system to a second part of the subject’s respiratory system.
  • one or more disclosed probiotics can inhibit and/or prevent the growth and/or spread of one or more pathogenic bacteria using competitive adherence and/or non-adherence mechanisms (e.g., secretion of antimicrobial factors). In an aspect, one or more disclosed probiotics can inhibit and/or prevent the adherence and/or colonization of one or more pathogenic bacteria. In an aspect, one or more disclosed probiotics can modulate the endocytosis or paracellular migration of one or more pathogenic bacteria. In an aspect, one or more disclosed probiotics can inhibit and/or prevent the spread of one or more pathogenic bacteria by competitive adherence and/or niche occupancy.
  • one or more disclosed probiotics can inhibit and/or prevent the growth and/or spread of S. pneumoniae using competitive adherence and/or non-adherence mechanisms (e.g., secretion of antimicrobial factors). In an aspect, one or more disclosed probiotics can inhibit and/or prevent the adherence and/or colonization of S. pneumoniae. In an aspect, one or more disclosed probiotics can modulate the endocytosis or paracellular migration of S. pneumoniae. In an aspect, one or more disclosed probiotics can inhibit and/or prevent the spread S. pneumoniae by competitive adherence and/or niche occupancy.
  • one or more disclosed probiotics can secrete one or more factors.
  • a disclosed secreted factor can be species-dependent and/or strain-dependent.
  • a disclosed secreted factor can inhibit and/or prevent the growth and/or spread of one or more pathogenic bacteria.
  • a disclosed secreted factor can inhibit and/or prevent the adherence and/or colonization of one or more pathogenic bacteria.
  • a disclosed secreted factor can modulate the endocytosis or paracellular migration of one or more pathogenic bacteria.
  • a disclosed secreted factor can inhibit and/or prevent the spread of one or more pathogenic bacteria by competitive adherence and/or niche occupancy.
  • a disclosed secreted factor can inhibit and/or prevent the growth and/or spread of S. pneumoniae.
  • a disclosed secreted factor can inhibit and/or prevent the adherence and/or colonization of S. pneumoniae.
  • a disclosed secreted factor can modulate the endocytosis or paracellular migration of S. pneumoniae.
  • a disclosed secreted factor can inhibit and/or prevent the spread of S. pneumoniae by competitive adherence and/or niche occupancy.
  • Corynebacterium sp., Dolosigranulum sp., Streptococcus sp., Lactobacillus sp., or any combination thereof can secrete one or more factors that inhibit and/or prevent the growth and/or spread of one or more pathogenic bacteria.
  • Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof can secrete one or more factors that inhibit and/or prevent the adherence and/or colonization of one or more pathogenic bacteria.
  • Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof can secrete one or more secreted factors that modulate the endocytosis or paracellular migration of one or more pathogenic bacteria.
  • Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof can secrete one or more secreted factors inhibit and/or prevent the spread of one or more pathogenic bacteria by competitive adherence and/or niche occupancy.
  • Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof can secrete one or more secreted factors inhibit and/or prevent the growth and/or spread of S. pneumoniae.
  • Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof can secrete one or more factors inhibit and/or prevent the adherence and/or colonization of S.
  • a disclosed method of modulating microbial diversity and/or composition Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof secrete one or more factors can modulate the endocytosis or paracellular migration of S. pneumoniae.
  • Corynebacterium sp ., Dolosigranulum sp ., Streptococcus sp ., Lactobacillus sp ., or any combination thereof can secrete one or more factors inhibit and/or prevent the spread of S. pneumoniae by competitive adherence and/or niche occupancy.
  • Corynebacterium sp. can secrete one or more factors that inhibit and/or prevent the growth and/or spread of one or more pathogenic bacteria. In an aspect of a disclosed method of modulating microbial diversity and/or composition, Corynebacterium sp. can secrete one or more factors that inhibit and/or prevent the adherence and/or colonization of one or more pathogenic bacteria. In an aspect of a disclosed method of modulating microbial diversity and/or composition, Corynebacterium sp. can secrete one or more secreted factors that modulate the endocytosis or paracellular migration of one or more pathogenic bacteria.
  • Corynebacterium sp. can secrete one or more secreted factors that inhibit and/or prevent the spread of one or more pathogenic bacteria by competitive adherence and/or niche occupancy.
  • Corynebacterium sp. can secrete one or more secreted factors that inhibit and/or prevent the growth and/or spread of S. pneumoniae. In an aspect of a disclosed method of modulating microbial diversity and/or composition, Corynebacterium sp. can secrete one or more factors that inhibit and/or prevent the adherence and/or colonization of S. pneumoniae. In an aspect of a disclosed method of modulating microbial diversity and/or composition, Corynebacterium sp. can secrete one or more factors that modulate the endocytosis or paracellular migration of S. pneumoniae. In an aspect of a disclosed method of modulating microbial diversity and/or composition, Corynebacterium sp. can secrete one or more factors that inhibit and/or prevent the spread of S. pneumoniae by competitive adherence and/or niche occupancy.
  • a disclosed method of modulating microbial diversity and/or composition can comprise a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any amount of inhibiting and/or preventing the growth and/or spread of one or more pathogenic bacteria (e.g., S. pneumoniae) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • pathogenic bacteria e.g., S. pneumoniae
  • a disclosed method of modulating microbial diversity and/or composition can comprise a 10-20%, 20-30%, 30-40%, 40-50%, 50-60%, 60- 70%, 70-80%, 80-90%, or 90-100% or any amount of inhibiting and/or preventing the growth and/or spread of one or more pathogenic bacteria (e.g., S. pneumoniae) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • pathogenic bacteria e.g., S. pneumoniae
  • a disclosed method of modulating microbial diversity and/or composition can comprise a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any amount of inhibiting and/or preventing the adherence and/or colonization of one or more pathogenic bacteria (e.g., S. pneumoniae) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • pathogenic bacteria e.g., S. pneumoniae
  • a disclosed method of modulating microbial diversity and/or composition can comprise a 10-20%, 20-30%, 30-40%, 40-50%, 50-60%, 60- 70%, 70-80%, 80-90%, or 90-100% or any amount of inhibiting and/or preventing the adherence and/or colonization of one or more pathogenic bacteria (e.g., S. pneumoniae) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • pathogenic bacteria e.g., S. pneumoniae
  • a disclosed method of modulating microbial diversity and/or composition can comprise a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any amount of modulating the endocytosis or paracellular migration of one or more pathogenic bacteria (e.g., S. pneumoniae ) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • pathogenic bacteria e.g., S. pneumoniae
  • a disclosed method of modulating microbial diversity and/or composition can comprise a 10-20%, 20-30%, 30-40%, 40-50%, 50-60%, 60- 70%, 70-80%, 80-90%, or 90-100% or any amount of modulating the endocytosis or paracellular migration of one or more pathogenic bacteria (e.g., S. pneumoniae ) when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • pathogenic bacteria e.g., S. pneumoniae
  • a disclosed method of modulating microbial diversity and/or composition can comprise a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any amount of inhibiting and/or preventing the spread of one or more pathogenic bacteria (e.g., S. pneumoniae ) by competitive adherence and/or niche occupancy when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • pathogenic bacteria e.g., S. pneumoniae
  • a control subject such as, for example, a subject that has not received a disclosed biotherapeutic
  • a disclosed method of modulating microbial diversity and/or composition can comprise a 10-20%, 20-30%, 30-40%, 40-50%, 50-60%, 60-70%, 70-80%, 80-90%, or 90-100% or any amount of inhibiting and/or preventing the spread of one or more pathogenic bacteria (e.g., S. pneumoniae ) by competitive adherence and/or niche occupancy when compared to a control subject (such as, for example, a subject that has not received a disclosed biotherapeutic).
  • pathogenic bacteria e.g., S. pneumoniae
  • a control subject such as, for example, a subject that has not received a disclosed biotherapeutic
  • a disclosed method of modulating microbial diversity and/or composition can comprise repeating the administering of one or more disclosed biotherapeutics, one or more disclosed secreted factors, a disclosed consortium of probiotics, one or more disclosed probiotics, or any combination thereof.
  • repeating the administering can comprise administering one or more times daily (e.g., 1, 2, 3, or 4 times).
  • repeating the administering can comprise administering on several consecutive days (e.g., for 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 days, or more than 10 days), weeks (e.g., for 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 weeks, or more than 10 weeks), or months (e.g., for 1, 2, 3, 4, 5, or 6 months, or more than 6 months).
  • a disclosed biotherapeutic, a disclosed secreted factor, a disclosed consortium of probiotics, a disclosed probiotic, or any combination thereof can be administered 1 - 3 times per day for about 7 to 21 days.
  • a disclosed method of modulating microbial diversity and/or composition can comprise monitoring the subject.
  • monitoring the subject can comprise monitoring the subject for the development of adverse effects.
  • a disclosed method of modulating microbial diversity and/or composition can comprise continuing to treat the subject.
  • continuing to treat the subject can comprise continuing to administer to the subject one or more disclosed biotherapeutics, one or more disclosed secreted factors, a disclosed consortium of probiotics, one or more disclosed probiotics, or any combination thereof.
  • a disclosed method of modulating microbial diversity and/or composition can comprise modifying one or more steps of the method.
  • modifying one or more steps of a disclosed method can comprise modifying the administering step.
  • modifying the administering step can comprise changing the amount of one or more disclosed biotherapeutics, one or more disclosed secreted factors, a disclosed consortium of probiotics, one or more disclosed probiotics, or any combination thereof administered to the subject, changing the frequency of administration of one or more disclosed biotherapeutics, one or more disclosed secreted factors, a disclosed consortium of probiotics, one or more disclosed probiotics, or any combination thereof, changing the duration of administration of one or more disclosed biotherapeutics, one or more disclosed secreted factors, a disclosed consortium of probiotics, one or more disclosed probiotics, or any combination thereof, changing the route of administration of one or more disclosed biotherapeutics, one or more disclosed secreted factors, a disclosed consortium of probiotics, one or more disclosed probiotics, or any combination thereof, or any combination of disclosed changes.
  • a disclosed method of modulating microbial diversity and/or composition can comprise manipulating the microbiome to inhibit and/or prevent infection caused by one or more pathogenic bacteria, such as an infection caused by S. pneumoniae.
  • a disclosed method of modulating microbial diversity and/or composition can comprise manipulating the microbiome to decrease and/or minimize the risk of infection caused by one or more pathogenic bacteria, such as an infection caused by S. pneumoniae.
  • the relative abundance of one or more disclosed Corynebacterium sp. is below a threshold level of 1.2 x 10 6 16S rRNA gene copies per biological sample, then the risk of colonization by S. pneumoniae is increased and/or higher and/or enhanced.
  • a disclosed method can further comprise administering and/or continuing to administer a therapeutically effective amount of a disclosed biotherapeutic.
  • a disclosed method can further comprise continuing to monitor the subject.
  • a disclosed method of promoting respiratory health can comprise manipulating the microbiome to inhibit and/or prevent infection caused by one or more pathogenic bacteria, such as an infection caused by S. pneumoniae.
  • a disclosed method of promoting respiratory health can comprise manipulating the microbiome to decrease and/or minimize the risk of infection caused by one or more pathogenic bacteria, such as an infection caused by S. pneumoniae. For example, in an aspect, when the relative abundance of one or more disclosed Corynebacterium sp. is below a threshold level of 1.2 x 10 6 16S rRNA gene copies per biological sample, then the risk of colonization by S. pneumoniae is increased and/or higher and/or enhanced.
  • a disclosed method can further comprise administering and/or continuing to administer a therapeutically effective amount of a disclosed biotherapeutic.
  • a disclosed method can further comprise continuing to monitor the subject.
  • the relative abundance of one or more disclosed Corynebacterium sp. when the relative abundance of one or more disclosed Corynebacterium sp. is less than about 50%, about 60%, about 70%, about 80%, or 90% of the microbiome, then the risk of colonization by S. pneumoniae is increased and/or higher and/or enhanced.
  • the relative abundance of one or more disclosed Corynebacterium sp. when the relative abundance of one or more disclosed Corynebacterium sp. is about 50% to about 60%, about 60% to about 70%, about 70% to about 80%, about 80% to about 90% of the microbiome, then the risk of colonization by S. pneumoniae is increased and/or higher and/or enhanced.
  • a disclosed method can further comprise administering and/or continuing to administer a therapeutically effective amount of a disclosed biotherapeutic.
  • a disclosed method can further comprise administering and/or continuing to administer a therapeutically effective amount of a disclosed biotherapeutic.
  • a disclosed method can further comprise administering and/or continuing to administer a therapeutically effective amount of a disclosed biotherapeutic.
  • when the relative abundance of Corynebacterium sp. is less than about 50%, about 60%, about 70%, about 80%, or 90% of the microbiome, then a disclosed method can further comprise administering and/or continuing to administer a therapeutically effective amount of a disclosed biotherapeutic.
  • the relative abundance of Corynebacterium sp. when the relative abundance of Corynebacterium sp.
  • a disclosed method can further comprise continuing to monitor the subject.
  • a disclosed method can further comprise continuing to monitor the subject.
  • a disclosed method of modulating microbial diversity and/or composition can comprise subjecting the subject to one or more invasive or non-invasive diagnostic assessments. Diagnostic assessments are known to the art.
  • a disclosed non-invasive diagnostic assessment can comprise x-rays, computerized tomography (CT) scans, magnetic resonance imaging (MRI) scans, ultrasounds, positron emission tomography (PET) scans, or any combination thereof.
  • a disclosed invasive diagnostic assessment can comprise a tissue biopsy or exploratory surgery.
  • techniques to monitor, measure, and/or assess the restoring one or more aspects of respiratory health can comprise qualitative (or subjective) means as well as quantitative (or objective) means. These means are known to the skilled person. For example, representative regulated variables and sensors relating to systemic homeostasis are discussed supra.
  • a disclosed biotherapeutic, a disclosed secreted factor, a disclosed consortium of probiotics, a disclosed probiotic, or any combination thereof can be administered in the absence of identifying the one or more pathogenic bacteria and/or in the absence of characterizing the microbiome.
  • a disclosed biotherapeutic, a disclosed secreted factor, a disclosed consortium of probiotics, a disclosed probiotic, or any combination thereof can be administered on demand.
  • a disclosed biotherapeutic can be formulated for administration as a pharmaceutical formulation.
  • a disclosed pharmaceutical formulation comprising a probiotic, a consortium of probiotics, factors secreted from a probiotic, factors secreted from a consortium of probiotics, or any combination thereof, and a pharmaceutically acceptable carrier and/or excipient can be used in any disclosed method of modulating microbial diversity and/or composition.
  • Any pharmaceutical formulation disclosed herein can be used in a disclosed method of modulating microbial diversity and/or composition.
  • kits comprising one or more of a disclosed biotherapeutic, a disclosed secreted factor, a disclosed consortium of probiotics, a disclosed probiotic, or any combination.
  • a disclosed kit can comprise a disclosed pharmaceutical formulation comprising a disclosed biotherapeutic, a disclosed secreted factor, a disclosed consortium of probiotics, a disclosed probiotic, or any combination thereof.
  • kits comprising at least one strain from the bacterial genus Corynebacterium.
  • a kit comprising at least one strain from the bacterial genus Dolosigranulum.
  • a kit comprising at least one strain from the bacterial genus Streptococcus.
  • a kit comprising at least one at least one strain from the bacterial genus Lactobacillus.
  • kits comprising at least one strain from the bacterial genus ( 'oryne bacterium , at least one strain from the bacterial genus Dolosigranulum , at least one strain from the bacterial genus Streptococcus , and at least one strain from the bacterial genus Lactobacillus.
  • kits comprising a pharmaceutical formulation comprising at least one Corynebacterium sp.
  • a kit comprising a pharmaceutical formulation comprising at least one Dolosigranulum sp.
  • a kit comprising a pharmaceutical formulation comprising at least one Streptococcus sp.
  • a kit comprising a pharmaceutical formulation comprising at least one Lactobacillus sp.
  • kits comprising a pharmaceutical formulation comprising at least one Corynebacterium sp ., at least one Dolosigranulum sp ., at least one Streptococcus sp ., and at least one Lactobacillus sp.
  • a disclosed kit can further comprise one or more anti -bacterial agents, one or more therapeutic agents, or any combination thereof.
  • Anti-bacterial agents and “Therapeutic Agents” are known to the art and are described supra.
  • anti -bacterial agents and combinations of anti -bacterial agents are known to the art and discussed supra in Part VII(C)(1).
  • the one or more disclosed biotherapeutics, disclosed secreted factors, disclosed consortiums of probiotics, disclosed probiotics, or any combination thereof can promote respiratory health in a subject, can reduce the risk of developing an infection caused by pathogenic bacteria, can reduce the risk of developing a S. pneumoniae infection in a subject, can treat and/or prevent S.
  • the one or more disclosed therapeutic agents in a disclosed kit can treat, prevent, inhibit, and/or ameliorate one or more comorbidities in a subject.
  • a disclosed kit can comprise at least two components constituting the kit. Together, the components constitute a functional unit for a given purpose (such as, for example, treating a subject diagnosed with or suspected of having an infection such as a respiratory infection). Individual member components may be physically packaged together or separately.
  • a kit comprising an instruction for using the kit may or may not physically include the instruction with other individual member components. Instead, the instruction can be supplied as a separate member component, either in a paper form or an electronic form which may be supplied on computer readable memory device or downloaded from an internet website, or as recorded presentation.
  • kits for use in a disclosed method can comprise (i) one or more of a disclosed biotherapeutic, a disclosed secreted factor, a disclosed consortium of probiotics, a disclosed probiotic, a disclosed pharmaceutical formulation, or any combination thereof, and (ii) a label or package insert with instructions for use.
  • suitable containers include, for example, bottles, vials, syringes, blister pack, etc.
  • the containers can be formed from a variety of materials such as glass or plastic.
  • the container can hold one or more of a disclosed biotherapeutic, a disclosed secreted factor, a disclosed consortium of probiotics, a disclosed probiotic, or any combination, a disclosed pharmaceutical formulation, or any combination thereof, and can have a sterile access port (for example the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle).
  • a sterile access port for example the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle.
  • the label or package insert can indicate one or more of a disclosed biotherapeutic, a disclosed secreted factor, a disclosed consortium of probiotics, a disclosed probiotic, or any combination, a disclosed pharmaceutical formulation, or any combination thereof can be used for promoting respiratory health in a subject, for reducing the risk of developing an infection caused by pathogenic bacteria, for reducing the risk of developing a S. pneumoniae infection in a subject, for treating and/or preventing S. pneumoniae colonization and/or infection, for modulating microbial diversity and/or composition, or any combination thereof.
  • a kit can comprise additional components necessary for administration such as, for example, other buffers, diluents, filters, needles, and syringes.
  • a disclosed kit can be used to promote respiratory health in a subject, to reduce the risk of developing an infection caused by pathogenic bacteria, to reduce the risk of developing a S. pneumoniae infection in a subject, to treat and/or prevent S. pneumoniae colonization and/or infection, to modulate microbial diversity and/or composition, or any combination thereof I. Miscellaneous
  • a method of preventing and/or reducing the risk of a respiratory infection in a subject comprising: (a) obtaining a biological sample from the subject; (b) generating a microbiome dataset based upon sequencing the microorganism portion of the sample; (c) determining the level of Cory neb acterium in the sample as compared to a control sample; and (d) increasing the relative abundance of Corynebacterium in the subject if the level of Corynebacterium is less than that of the control.
  • the respiratory infection can comprise bacterial pneumonia.
  • a disclosed bacterial pneumonia can be caused by Staphylococcus aureus including but not limited to methicillin-resistant Staphylococcus aureus (MRS A), Streptococcus pneumoniae (S.
  • the bacterial pneumonia can be caused by S. pneumoniae.
  • a disclosed biological sample can comprise a nasal swab or nasal lavage.
  • a disclosed microbiome can comprise the nasopharyngeal microbiome.
  • a method of determining the risk of a subject developing a respiratory infection comprising: (a) obtaining a biological sample from the subject; (b) generating a microbiome dataset based upon sequencing the microorganism portion of the sample; (c) determining the level of Corynebacterium in the sample as compared to a control sample wherein a relative abundance of Corynebacterium of less than that of the control is indicative of a higher likelihood of developing a respiratory infection; and (d) increasing the relative abundance of Corynebacterium in the subject if the level of Corynebacterium is less than that of the control.
  • the respiratory infection can comprise bacterial pneumonia.
  • a disclosed bacterial pneumonia can be caused by Staphylococcus aureus including but not limited to methicillin-resistant Staphylococcus aureus (MRS A), Streptococcus pneumoniae (S.
  • bacterial pneumonia can be caused by S. pneumoniae.
  • a disclosed biological sample can comprise a nasal swab or nasal lavage.
  • a disclosed microbiome can comprise the nasopharyngeal microbiome.
  • a method of preventing and/or reducing the risk of a respiratory infection in an infant subject comprising: (a) obtaining a biological sample from the subject; (b) generating a microbiome dataset based upon sequencing the microorganism portion of the sample; (c) determining the level of Corynebacterium in the sample as compared to a control sample; and (d) increasing the relative abundance of Corynebacterium in the subject by administering breast milk to the subject if the level of Corynebacterium is less than that of the control.
  • the respiratory infection can comprise bacterial pneumonia.
  • a disclosed bacterial pneumonia can be caused by Staphylococcus aureus including but not limited to methicillin-resistant Staphylococcus aureus (MRS A), Streptococcus pneumoniae (S. pneumoniae) including penicillin-resistant Streptococcus pneumoniae (PRSP), Haemophilus influenzae , Moraxella catarrhalis , Klebsiella pneumoniae , Legionella pneumophila , Chlamydophila pneumoniae , Mycoplasma pneumoniae , Chlamydophila psittaci , Coxiella burnetii , Escherichia coli , or any combination thereof.
  • Staphylococcus aureus including but not limited to methicillin-resistant Staphylococcus aureus (MRS A), Streptococcus pneumoniae (S. pneumoniae) including penicillin-resistant Streptococcus pneumoniae (PRSP), Haemophilus influenzae , Moraxella catarrhalis , Klebs
  • the bacterial pneumonia can be caused by S. pneumoniae.
  • a disclosed biological sample can comprise a nasal swab or nasal lavage.
  • a disclosed microbiome can comprise the nasopharyngeal microbiome.
  • Streptococcus pneumoniae (also known as pneumococcus) is a leading cause of severe infections among children and adults, with the highest incidence of pneumococcal disease occurring during infancy (1).
  • S. pneumoniae causes a broad range of infections ranging from mild respiratory illnesses, such as acute otitis media and acute sinusitis, to invasive pneumococcal disease (IPD), which includes serious illnesses such as bloodstream infection and meningitis (Bogaert D, et al (2004) Lancet Infect Dis. 4(3): 144-154).
  • IPD invasive pneumococcal disease
  • S. pneumoniae is responsible for more than 300,000 child deaths each year, the overwhelming majority of which result from pneumonia (Wahl B, et al. (2016) Lancet Glob Health.
  • a complex microbial community resides in the upper respiratory tract and has co-evolved with humans (Zaneveld J, et al. (2008) Curr Opin Chem Biol. 12(1): 109-114). Over the last decade, accumulating evidence has emerged for this microbiome’s role in the pathogenesis of respiratory infections (de Steenhuijsen Piters WA, et al. (2020) Cell Host Microbe. 28(2):223- 232), with microbial communities at distinct anatomical sites within the upper respiratory tract contributing to resistance to colonization or infection by specific pathogens. Within the nasopharynx, resident microbes may resist colonization by S.
  • H. influenzae can inhibit S. pneumoniae by downregulating expression of pneumococcal adherence factors (Cope EK, et al. (2011) PloS one. 6(12):e28523) or by stimulating complement-dependent phagocytosis of S. pneumoniae (Lysenko ES, et al. (2005) PLoS pathogens.
  • colonization of the nasopharynx is a necessary precursor to infections caused by S. pneumoniae , and is particularly prevalent among young children.
  • the nasopharyngeal microbiome undergoes rapid shifts in composition during early childhood (39- 41), primarily driven by environmental factors, such as delivery mode (42, 43), infant feeding practices (41, 44), contact with other children (39), season (40, 45), and antibiotic exposures (39).
  • Previous studies that evaluated associations between the nasopharyngeal microbiome and S. pneumoniae colonization in children were cross-sectional (6, 32, 33), and few data are available from low- and middle-income countries, where >80% of child deaths from S.
  • This study sought to identify interspecies interactions that modify the risk of pneumococcal colonization during infancy and to describe nasopharyngeal microbiome development during the first year of life in a sub-Saharan African setting.
  • the nasopharyngeal microbiomes of 179 mother-infant dyads in Botswana was studied using 16S ribosomal RNA (rRNA) gene sequencing and S. pneumoniae colonization with a species-specific PCR assay was identified.
  • rRNA ribosomal RNA
  • This work identified changes in microbiome diversity and composition during infancy, evaluated associations between the nasopharyngeal microbiome and pneumococcal colonization risk, and identified environmental factors that influenced nasopharyngeal microbiome composition during infancy.
  • Botswana is a landlocked country in southern Africa with a semi-arid climate and a rainy summer season that typically occurs from November to March.
  • the country’s under-five child mortality rate was estimated to be 41.6 per 1,000 live births in 2019 (UN Inter-agency Group for Child Mortality Estimation. Levels & trends in child mortality, report 2020).
  • Haemophilus influenzae type B (Hib) and 13 -valent pneumococcal conjugate (PCV-13) vaccinations were included in the national immunization program in November 2010 and July 2012, respectively.
  • Complete vaccine series coverage rates in 2019 were estimated to be 95% for Hib and 92% for PCV-13 (United Nations Children’s Fund, World Health Organization.
  • Botswana WHO and UNICEF estimates of immunization coverage, 2019 revision). Botswana’s capital and largest city, Gaborone, is in the country’s South-East district and has a population of 231,626 based on a census conducted in 2011 (Statistics Botswana. 2011 Population and Housing Census Analytical Report).
  • Exclusion criteria included maternal age less than 18 years, infant birth weight less than 2,000 g, multiple gestation pregnancy, and caesarian delivery. Participants were seen for monthly study visits until the infant was six months of age and every other month thereafter until the infant was 12 months of age. At all study visits, a caregiver questionnaire was administered, and nasopharyngeal swabs were collected from mothers and infants by trained study personnel. Nasopharyngeal samples were placed directly into MSwab medium (Copan Italia), transported to the National Health Laboratory in Gaborone, and frozen within 4 hours of collection to -80 °C. Testing for S. pneumoniae was performed using a quantitative PCR assay targeting the autolysin gene ⁇ lytA ⁇ as previously described (6, 84).
  • a dried blood spot was collected from HIV-exposed infants by heel prick at two months of age and, for infants who were breastfed for any duration, again at 12 months of age. These samples were tested for HIV-1 DNA using the Cobas AmpliPrep/Cobas TaqMan HIV-1 Qualitative Assay, version 2.0 (Roche) (Gueye SB, et al. (2016) J Virol Methods. 229:12-15). All study participants or their legal guardians provided written informed consent to participate in this study. The study protocol was approved by the Botswana Ministry of Health, the Princess Marina Hospital ethics committee, and institutional review boards at the University of Pennsylvania, Children’s Hospital of Philadelphia, McMaster University, and Duke University.
  • the Duke Microbiome Core Facility extracted DNA from nasopharyngeal samples using Powersoil Pro extraction kits (Qiagen) following the manufacturer’s instructions. DNA concentrations were determined using Qubit dsDNA high-sensitivity assay kits (Thermo Fisher Scientific). Negative extraction and PCR controls were amplified with all four batches of samples included in analyses to evaluate for background contamination. For the first two sample batches, these negative controls were verified to not have visible bands on gel electrophoresis. For the final two sample batches, sequencing was performed on these negative control samples.
  • Bacterial community composition was characterized by PCR amplification of the V4 variable region of the 16S rRNA gene using the forward primer 515 and the reverse primer 806 following the Earth Mi crobiome Project protocol (Gilbert JA, et al. (2010) Stand Genomic Sci. 3(3):243- 248). These primers carry unique barcodes that allow for multiplexed sequencing. Equimolar 16S rRNA PCR products from all samples were quantified and pooled prior to sequencing. Sequencing was performed by the Duke Sequencing and Genomic Technologies Core Facility on a MiSeq instrument (Illumina, Inc.) configured for 250 base-pair paired-end sequencing. Raw sequences were trimmed using Trimmomatic version 0.36 (Bolger AM, et al.
  • Sequencing reads were classified into 7,167 AS Vs representing 200 genera from 8 phyla.
  • a standard nucleotide REFSEQ BLAST search was performed using the National Center for Biotechnology Information’s Bacteria and Archaea 16S ribosomal RNA project database (Camacho C, et al. (2009) BMC Bioinformatics. 10:421). Species information was assigned to ASVs using a best-hit approach based on the E value with a minimum percent identity of 97%.
  • Alpha Shannon and Chaol indices
  • beta diversity Bray-Curtis dissimilarity
  • Phyloseq R package version 1.36.0 McMurdie PJ, et al. (2013) PloS one. 8(4):e612157.
  • Wilcoxon signed-rank tests were used to compare microbiome alpha diversity across infant ages and between paired infant and maternal samples.
  • negative binomial mixed effect models with subject as a random effect were used to account for repeated sampling of individuals.
  • Beta diversity with PERMANOVA was comparedusing the adonis function within the vegan R package version 2.5.7 (Oksanen J, et al. (2007) Community Ecology Package.
  • ASVs were aggregated at the genus level. Samples were classified as dominated when 50% or more of the sequencing reads generated from this sample were assigned to a single genus. Samples dominated by a genus other than the six most highly abundant genera were classified in a single “other” category. Samples for which no single genus accounted for the majority of the sequencing reads were classified as “biodiverse.” A sample’s microbiome profile was considered to be “stable” when the next visit’s sample from that infant was classified as the same biotype. Logistic regression was then used to evaluate associations between specific nasopharyneal biotypes and microbiome stability, adjusting for infant age in days.
  • MaAsLin2 version 1.6.0 (MallickH, et al. (2021) bioRxiv. 2021.03.28.437378) was used to fit log-transformed linear mixed models evaluating associations between sociodemographic factors and environmental exposures and the relative abundances of bacterial genera within the infant nasopharyngeal microbiome. These analyses considered the following variables identified based on a literature review: sex, low birth weight ( ⁇ 2500 g), HIV exposure status, location of residence (urban vs. rural), household use of solid fuels, number of other child household members ( ⁇ 5 years of age), season (summer vs.
  • MaAsLin2 analyses were limited to bacterial genera present in at least 10% of nasopharyngeal samples. The comparisons were corrected for the false discovery rate using the Benjamini-Hochberg procedure and a q value threshold for significance of 0.20. The models included subject as a random effect. To identify compositional features of the nasopharyngeal microbiome that influence the risk of pneumococcal colonization, a Cox proportional hazards model was fit evaluating the association between nasopharyngeal microbiome biotype and S. pneumoniae colonization detected at the subsequent study visit.
  • Corynebacterium strains from infant nasopharyngeal samples 10 pL of sample were streaked on plates containing brain heart infusion (BHI) medium (Sigma-Aldrich) supplemented with 50 pg/mL of fosfomycin disodium (Fisher Scientific) and 1% Tween 80 (VWR). Single bacterial colonies were subcultured to 5% sheep blood agar plates (Fisher Scientific) and identified bacterial species using a VITEK MS automated mass spectrometry microbial identification system (bioMerieux). Cell-free growth inhibition assays were used to screen Corynebacterium strains for the secretion of anti-pneumococcal factors.
  • Corynebacterium strains were grown in either 20 mL of BHI medium supplemented with 0.2% Tween 80 for 12-18 hours at 37 °C and 5% CO2. These cultures were centrifuged at 3000 rpm for 10 minutes to generate cell pellets, and the supernatants were sterile-filtered with a 0.22-mM filter. The resulting cell-free media was diluted 50% in tryptic soy broth (TSB; Fisher Scientific) and glycerol stocks of two strains of S. pneumoniae , one a reference strain (ATCC 6303; serotype 3) and the second strain isolated from an infant nasopharyngeal sample (05-160; serotype 11 A), were separately diluted 1:50 into the diluted cell-free media. Growth was assessed by OD600 readings relative to blank media controls for each growth medium over 24 hours.
  • the Nasopharyngeal Microbiome was a Low-Diversity Microbial Community Throughout Infancy
  • Nasopharyngeal swab samples were collected monthly (0-6 months) or bimonthly (6-12 months) from 179 mother-infant dyads recruited at urban and rural study sites in southern Botswana. Infants were bom vaginally, had a median [interquartile range (IQR)] birth weight of 3120 grams (2855 grams, 3408 grams), and were predominantly breastfed (Table 3). [0346] Table 3 - Characteristics of the 179 Mother-Infant Dyads Included in the Study Population. [0347] Infants were followed in this study to a median (IQR) age of 12.0 (8.0, 12.1) months.
  • Infant nasopharyngeal microbiome diversity remained relatively stable during infancy and similar to maternal nasopharyngeal microbiome diversity (FIG. 1A - FIG. IB), except at birth (10), when diversity was higher than later in infancy (Wilcoxon signed-rank tests, » ⁇ 0.0001) and compared to maternal samples (Wilcoxon signed-rank test, p ⁇ 0.0001).
  • Nasopharyngeal microbiome richness increased with age during infancy (negative binomial regression,/» ⁇ 0.0001) and did not differ from the richness of the maternal nasopharyngeal microbiome after five months of age (Wilcoxon signed-rank tests,/» > 0.05).
  • a per sample microbiome profile was considered “stable” when the next sample from that infant was classified as the same biotype. Based on this definition, within-infant stability of the nasopharyngeal microbiome varied by biotype (FIG. 3A - FIG. 3C and Table 6).
  • MaAsLin2 (52) was used to fit generalized linear mixed models evaluating associations between sociodemographic factors and environmental exposures and the abundances of specific bacterial genera within the nasopharyngeal microbiome (Table 7).
  • S. pneumoniae colonization was identified in 144 of 179 (80%) infants at a median (IQR) age of 71 (39, 126) days (FIG. 6).
  • IQR median age of 71 (39, 126) days
  • Cox proportional hazards model was first fit to evaluate associations between nasopharyngeal microbiome biotypes and acquisition of S. pneumoniae at the next study visit (Table 8).
  • Table 9 Cox Proportional Hazards Model Analyses Evaluating the Association Between the Relative Abundance of Corynebacterium in Infant Nasopharyngeal Samples and the Risk of Acquisition of S. pneumoniae Prior to the Next Study Visit.
  • this low- diversity microbial community was typically comprised mostly of bacteria from six genera, with Corynebacterium and Staphylococcus predominating during the first several months of life and Dolosigranulum and Moraxella becoming more abundant later in infancy (Teo SM, et al. (2015) Cell Host Microbe. 17(5):704-715; Mika M, et al. (2015) J Allergy Clin Immunol. 135(4):905- 912. el 1). These trends in nasopharyngeal microbiome composition during infancy appeared to be highly conserved despite substantial differences in host characteristics, household exposures, and climate.
  • the nasopharyngeal microbiome of infants in Botswana was found to be highly dynamic, although microbiome stability varied markedly based on the dominant genus. In particular, higher microbiome stability was observed with nasopharyngeal microbiome profiles that were dominated by Moraxella , while lower stability was seen with profiles that were dominated by Dolosigranulum , Haemophilus , or Streptococcus. Findings from studies conducted in high- income countries were broadly similar, although notably nasopharyngeal microbiome profiles with high abundance of Dolosigranulum were reported to be highly stable in these settings (39, 41). Further research is needed to investigate associations between the presence and abundance of Dolosigranulum in the nasopharyngeal microbiome and child respiratory health in low- and middle-income countries.
  • Feeding practices also influenced the composition of the nasopharyngeal microbiome of infants in this study, with breastfeeding promoting the enrichment of the nasopharyngeal microbiome with Corynebacterium spe cies.
  • Corynebacterium is a diverse bacterial genus that includes common residents of the upper respiratory tracts, skin, and gastrointestinal tracts of humans and animals. Although more than 150 species of Corynebacterium have been identified to date (68), the most common species isolated from the human respiratory tract are C. accolens , C. pseudodiphtheriticum, C. propinquum, C. striatum , and C. tuberculostearicum (56-58).
  • Corynebacterium diphtheriae the etiological agent of diphtheria (69), Corynebacterium .species only rarely cause human disease, often in the setting of compromised host immunity (70, 71), indwelling prosthetic material (71-73), or chronic respiratory diseases (Renom F, et al. (2014) New Microbes New Infect. 2(4): 106-114; Bittar F, et al. (2010) Emerg Infect Dis. 16(8): 1231).
  • This low pathogenicity of non-diphtheriae Corynebacterium .species is a key characteristic that supports their further evaluation for use as biotherapeutics.
  • Bomar et al. identified a C. accolens strain that inhibited S. pneumoniae through the production of a lipase that releases antipneumococcal free fatty acids from human skin triacylglycerols (33).
  • Serial NP samples were from 300 infants ( ⁇ 12 months of age) enrolled in a prospective cohort study in Botswana. Sp colonized more than half (54%) of infants by 2 months of age - the age for the first dose of 13-valent pneumococcal conjugate vaccine (PCV-13) - and Sp colonized more than 85% by age 12 months.
  • PCV-13 13-valent pneumococcal conjugate vaccine
  • Pneumonia leads among infectious causes of death among children, accounting for more than 800,000 deaths in 2017. Bacterial pathogens, particularly S. pneumoniae (Sp), associate with the highest mortality. Pneumococcal conjugate vaccines effectively prevent invasive diseases like meningitis and bacteremia caused by vaccine serotypes. (Waight PA, et al. (2015) Lancet Infect Dis. 15(6):629; Moore MR, et al. (2015) Lancet Infect Dis. 15(3):301-309). However, these vaccines are less effective in preventing Sp pneumoniae and other respiratory infections. (Cutts FT, et al. (2005) Lancet. 365(9465): 1139-1146; Klugman KP, et al.
  • NP Nasopharyngeal
  • Corynebacterium spp. can Inhibit Colonization by Bacterial Respiratory Pathogens.
  • Previous studies demonstrate that Corynebacterium spp. antagonize several important pathobionts.
  • C. propinquum was recently recognized to inhibit the growth of staphylococci by iron restriction through siderophore production.
  • Stubbendieck RM et al. (2019) Appl Environ Microbiol. 85(10)
  • intranasal administration of a C. pseudodiphtheriticum strain effectively eradicated S. aureus nasal carriage in adults, demonstrating the biotherapeutic potential of Corynebacterium spp.
  • Kiryukhina NV et al.
  • the work described herein focuses on adherence as a mechanism by which Corynebacterium spp. colonize the respiratory epithelium and competitively exclude Sp (FIG. 11A - FIG. 11B).
  • adherence of Corynebacterium strains isolated from the human respiratory tract and a non-respiratory source (skin) are measured in models for different parts of the human respiratory tract.
  • the ability of strains isolated from the respiratory tract to inhibit respiratory epithelium adherence and invasion by Sp is evaluated. Genome-wide association analyses are used to identify genomic-phenotypic relationships for epithelium adherence.
  • the work described herein also focuses on non-adherence mechanisms by which Corynebacterium spp. inhibit Sp colonization (FIG.
  • Cell-free Corynebacterium supernatants are sceened for secreted inhibitory factors active against Sp. Comparative proteomics are employed to identify Corynebacterium- secreted proteins that inhibit or kill Sp. Supernatants from Corynebacterium-exposed respiratory epithelium are also screened for Sp inhibition to identify strains that stimulate the release of host-derived Sp-inhibitory factors.
  • Respiratory isolates of Corynebacteria exhibit high respiratory epithelium adherence and exclude Sp through competitive binding at the epithelial surface.
  • the key experiments include the following. First, adherence of Corynebacterium strains from the respiratory tract and skin are quantified in human respiratory epithelium tissue models. Second, whole-genome sequencing, assembly, and genome annotation are performed. Third, comparative genomics are used to identify genes that are associated with adherence to respiratory epithelium. Fourth, competitive Corynebacterium- Sp adherence experiments are performed for Corynebacterium strains that adhere to respiratory epithelium.
  • Adherence by Corynebacterium to the respiratory epithelium is fundamental to colonization and persistence. Corynebacterium is expected to differentially adhere to distinct areas of the respiratory epithelium. The adherence of 250 strains from the disclosed biorepository is measured to model upper and lower respiratory epithelium using respiratory epithelium cells RMPI 2650 (human nasal carcinoma, ATCC CCL-30), Detroit 562 (human pharyngeal carcinoma; ATCC CCL-138), and A549 cells (human lung carcinoma; ATCC CCL-185), respectively, using the previously described assays (see, e.g., FIG. 8).
  • Corynebacterium spp. can exclude or control Sp in the human nasopharynx through competitive adherence and niche occupancy.
  • competitive adherence assays are performed (see, for example, FIG. 8) with each of the 250 Corynebacterium strains and two Sp strains (serotype 3, ATCC 6303; serotype 6b, ATCC 700675).
  • the rationale fortesting two different Sp strains is to increase the likelihood that any competitive advantage of a Corynebacterium strain is not unique to one Sp type.
  • the top ten strains for percent adherence are prioritized for further measurements of adherence and competitive exclusion of Sp using differentiated, polarized human primary upper respiratory nasal and pharyngeal cells (PromoCell). Differentiated, polarized primary cells are used to confirm the adherence and competition of Corynebacterium phenotypes of interest on an epithelium to more closely resembling the native normal upper respiratory epithelium.
  • Corynebacterium isolates can also inhibit Sp transepithelial invasion by blocking Sp adherence or independently modulating Sp endocytosis or paracellular migration.
  • Detroit 562 cells are grown to confluence in 3-micron PET transwell units for ten days, measuring transepithelial resistance for polarization.
  • Controls 1 include no added Corynebacteria or Sp and control epithelial cells treated with 100 mM dynasore (Sigma Aldrich) and 7.5 pg/mL nystatin (Sigma Aldrich) as Sp endocytosis inhibitors. (Weight CM, et al. (2019) Nat Commun. 10(1):3060). Corynebacterium strains of interest preclude Sp from invading into the basal chamber. Biological and technical triplicates are performed.
  • GenBank does not contain complete genomes for strains from any of the species of Corynebacterium that are most commonly isolated from the human respiratory tract. Therefore, for all species in the disclosed biorepository for which a complete genome is unavailable in GenBank, a representative strain is selected to generate a complete genome sequence.
  • Extracted DNA (Lucigen Masterpure) are prepared for Illumina compatible sequencing libraries using iGenomx Riptide and short read sequenced on the Northwestern NUSeq core Illumina NovaSeq 6000 instrument (150 bp paired-end reads, 60-100x coverage). Long-read sequencing are performed on an Oxford Nanopore Minion.
  • Genome assemblies are performed (Canu), polished (Arrow), and annotated for open-reading frames, virulence factors, and antibiotic resistance genes (DFAST; Abricate).
  • DFAST antibiotic resistance genes
  • psortb are used to make in silico predictions of gene product cellular localization, which help to focus on potential surface-associated factors and predicted secreted factors.
  • a pangenome analysis (with methods described herein and in FIG. 10) are performed using these new de novo assemblies and the publicly available draft and complete genomes meeting the criteria of having total base and open-reading frame counts within 2 standard deviations of the mean (currently 673 genomes classified in the genus Corynebacterium meet these criteria).
  • Gene clusters are defined as those with pblast scores less than 10 8 and > 75% gene coverage.
  • Core genes are defined as those genes in 100% of all genomes.
  • Shared accessory genes are defined as genes represented in 6-99% of the genomes. Specific genes are defined as genes in ⁇ 5% of genomes.
  • BWA is used to map short sequencing reads to the Corynebacterium pan-genome.
  • treeWAS is employed to test for associations between the gene content of Corynebacterium strains and the degree of (i) respiratory epithelium adherence, (ii) Sp inhibition through competitive adherence, (iii) inhibition of Sp invasion, and (iv) epithelial viability measures.
  • Each variable is used as continuous data.
  • treeWAS is specifically designed for microbial genome wide association data.
  • Comparative genomics identifies accessory genes that encode specific surface pili and adhesins that likely mediate adherence of Corynebacterium spp. to the human respiratory epithelium. Moreover, a subset of these adhesive factors correlates with competitive adherence of Sp. The presence (or absence) of these genes explains observed strain-level differences in the studied phenotypes. The results of the Sp adherence and invasion assays are used to select specific Corynebacterium strains for further study as candidate biotherapeutics.
  • a high degree of genetic variation across strains and species can preclude the identification of specific genes or gene variants that are associated with phenotypes using a whole-genome association approach.
  • An alternative approach involves limiting comparative analyses to genes known to encode adhesive factors, such as pili or adhesins.
  • culturing strains from clinical samples collected from several patient populations and ecological niches are employed.
  • strains from some regions with high child pneumonia mortality are not currently available but can be collected through established research collaborations.
  • This research provides substantial new genomic and phenotypic knowledge about non- diphtheriae Corynebacterium and how different species adapted to compete with the global pathogen Sp. Through newly discovered mechanisms elucidated herein by which Corynebacterium spp. colonize the respiratory tract and inhibit pathogen colonization and growth, potential biotherapeutics, including probiotics and antimicrobial factors, are identified. This research can ultimately lead to developing the first rationally-designed NP-delivered probiotics for pneumonia prevention, which can substantially impact global child mortality.
  • Mass spectra are generated on most potent inhibitory and non-inhibitory (control) supemants to identify bacterial and host proteins that mediate Sp inhibition. Spectra are analyzed using Mascot (Matrix Science) and the National Center for Biotechnology Information’s non- redundant protein (nr) database. Peptide and protein identifications are validated using Scaffold (Proteome Software, Inc.). The false discovery rate for peptide-spectrum matching and protein identification are set at 1 % and determined using the target-decoy search strategy. (Elias JE, et al. (2010) Methods Mol Biol. 04:55-71). Peptide identifications are accepted if established at > 95.0% probability using PeptideProphet.
  • Sterile 0.2-micron filtered cell-free tissue culture supernatants are co-incubated with the Sp reference strains at a 1:1 ratio in BHI medium.
  • a 1:1 ratio of BHI and tissue culture medium are used as a negative control and BHI with human b- defensin-2 serve as a positive inhibition control.
  • Growth of Sp is monitored continuously by OD600 with shaking at 37 °C for 8 hours.
  • Peptides are identified in the Northwestern Proteomics Facility using LC/MS that are uniquely present in the inhibitory supernatants and produced by human respiratory epithelium (to differentiate from bacterial proteins). Where available commercially or possible through synthesis, recombinant factors are tested to recapitulate and validate the inhibition.
  • the work described herein identifies lantibiotics that are secreted by Corynebacterium strains and that inhibit Sp.
  • Corynebacterium strains that stimulate the release of defensins from human epithelial surfaces as a mechanism of inhibition of Sp adherence and growth are identified.
  • the data generated herein enable the selection of Corynebacterium strains based on potency of Sp inhibition for further investigation as biotherapeutics.
  • knowledge of these genetic mechanisms is used to bioengineer other commensal bacteria for use as probiotics for respiratory infection prevention.
  • Preliminary data point towards peptide inhibitors of Sp by Corynebacterium .s/ip but do not exclude non peptide molecules.
  • non-targeted mass spectrometry is employed.
  • Strains are also subjected to random transposition (Lucigen In Vivo Transposom Complexes) and screened for mutants with attenuation in the secreted Sp inhibition activity.
  • nasopharyngeal swabs were collected monthly (0-6 months of age) or bimonthly (6-12 months of age) from 179 mother-infant dyads in Botswana.
  • 16S ribosomal RNA gene sequencing was used to characterize the nasopharyngeal microbiome and identified S. pneumoniae colonization using a species-specific PCR assay.
  • pneumoniae colonization was detected in 144 (80%) infants at a median age of 71 days and a strong negative association between the relative abundance of the bacterial genera Corynebacterium within the infant nasopharyngeal microbiome and the risk of S. pneumoniae colonization was identified.
  • Using in vitro cultivation experiments growth inhibition of S. pneumoniae by secreted factors from strains of several Corynebacterium spe cies isolated from these infants was demonstrated. Finally, it was demonstrated that antibiotic exposures and the winter season are associated with a decline in the relative abundance of Corynebacterium within the nasopharyngeal microbiome, while breastfeeding was associated with an increase in the Corynebacterium relative abundance.

Landscapes

  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Veterinary Medicine (AREA)
  • Public Health (AREA)
  • Animal Behavior & Ethology (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Engineering & Computer Science (AREA)
  • Medicinal Chemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Microbiology (AREA)
  • Pulmonology (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • General Chemical & Material Sciences (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Mycology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Molecular Biology (AREA)
  • Analytical Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Otolaryngology (AREA)
  • Epidemiology (AREA)
  • General Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Biophysics (AREA)
  • Biotechnology (AREA)
  • Genetics & Genomics (AREA)
  • Immunology (AREA)
  • Biochemistry (AREA)
  • Medicines Containing Material From Animals Or Micro-Organisms (AREA)

Abstract

Sont divulgués ici des agents biothérapeutiques comprenant des probiotiques ou un groupe de probiotiques. Sont divulgués ici des agents biothérapeutiques comprenant des facteurs sécrétés par des probiotiques ou des facteurs sécrétés par un groupe de probiotiques. Sont également divulgués ici des formulations pharmaceutiques comprenant un agent biothérapeutique divulgué. Sont également divulgués ici des méthodes de promotion de la santé respiratoire, de réduction du risque de développement et d'infection, de traitement et/ou de prévention d'une colonisation bactérienne et/ou d'une infection bactérienne, et de modulation de la diversité et/ou de la composition microbienne.
PCT/US2022/073367 2021-07-01 2022-07-01 Compositions et méthodes permettant de favoriser la santé respiratoire WO2023279093A1 (fr)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US202163217384P 2021-07-01 2021-07-01
US63/217,384 2021-07-01

Publications (1)

Publication Number Publication Date
WO2023279093A1 true WO2023279093A1 (fr) 2023-01-05

Family

ID=84690713

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2022/073367 WO2023279093A1 (fr) 2021-07-01 2022-07-01 Compositions et méthodes permettant de favoriser la santé respiratoire

Country Status (1)

Country Link
WO (1) WO2023279093A1 (fr)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US11654165B2 (en) 2020-05-28 2023-05-23 Trench Therapeutics, Inc. Airway medicaments

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2012168732A1 (fr) * 2011-06-10 2012-12-13 Dupont Nutrition Biosciences Aps Traitement d'une maladie des voies respiratoires à l'aide de bifidobacterium lactis bl-04
WO2017189846A1 (fr) * 2016-04-27 2017-11-02 Thaddeus Stappenbeck Méthodes de pronostic de la maladie de crohn, comportant la défensine 5 humaine (hd5)

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2012168732A1 (fr) * 2011-06-10 2012-12-13 Dupont Nutrition Biosciences Aps Traitement d'une maladie des voies respiratoires à l'aide de bifidobacterium lactis bl-04
WO2017189846A1 (fr) * 2016-04-27 2017-11-02 Thaddeus Stappenbeck Méthodes de pronostic de la maladie de crohn, comportant la défensine 5 humaine (hd5)

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
BRUGGER SILVIO D., ESLAMI SARA M., PETTIGREW MELINDA M., ESCAPA ISABEL F., HENKE MATTHEW T., KONG YONG, LEMON KATHERINE P.: "Dolosigranulum pigrum Cooperation and Competition in Human Nasal Microbiota", MSPHERE, vol. 5, no. 5, 28 October 2020 (2020-10-28), XP093021641, DOI: 10.1128/mSphere.00852-20 *
ORTIZ MOYANO RAMIRO, RAYA TONETTI FERNANDA, TOMOKIYO MIKADO, KANMANI PAULRAJ, VIZOSO-PINTO MARÍA GUADALUPE, KIM HOJUN, QUILODRÁN-V: "The Ability of Respiratory Commensal Bacteria to Beneficially Modulate the Lung Innate Immune Response Is a Strain Dependent Characteristic", MICROORGANISMS, vol. 8, no. 5, 13 May 2020 (2020-05-13), pages 727, XP093021643, DOI: 10.3390/microorganisms8050727 *

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US11654165B2 (en) 2020-05-28 2023-05-23 Trench Therapeutics, Inc. Airway medicaments

Similar Documents

Publication Publication Date Title
Nicola et al. Characterization of the upper and lower respiratory tract microbiota in Piedmontese calves
Waites et al. Mycoplasma pneumoniae from the respiratory tract and beyond
Mandell et al. Canadian guidelines for the initial management of community-acquired pneumonia: an evidence-based update by the Canadian Infectious Diseases Society and the Canadian Thoracic Society
Mandell et al. Update of practice guidelines for the management of community-acquired pneumonia in immunocompetent adults
Allen et al. Characterization of the nasopharyngeal microbiota in health and during rhinovirus challenge
Smith et al. Respiratory syncytial virus increases the virulence of Streptococcus pneumoniae by binding to penicillin binding protein 1a. A new paradigm in respiratory infection
Murphy et al. Persistent colonization by Haemophilus influenzae in chronic obstructive pulmonary disease
Campisi et al. Genomic analysis reveals multi-drug resistance clusters in group B Streptococcus CC17 hypervirulent isolates causing neonatal invasive disease in southern mainland China
Croucher et al. Dominant role of nucleotide substitution in the diversification of serotype 3 pneumococci over decades and during a single infection
Suárez-Arrabal et al. Nasopharyngeal bacterial burden and antibiotics: influence on inflammatory markers and disease severity in infants with respiratory syncytial virus bronchiolitis
Giufrè et al. Carriage of Haemophilus influenzae in the oropharynx of young children and molecular epidemiology of the isolates after fifteen years of H. influenzae type b vaccination in Italy
Ubukata et al. Genetic characteristics and antibiotic resistance of Haemophilus influenzae isolates from pediatric patients with acute otitis media after introduction of 13-valent pneumococcal conjugate vaccine in Japan
Kainuma et al. An outbreak of fluoroquinolone-resistant Pseudomonas aeruginosa ST357 harboring the exoU gene
Torres et al. Bacterial pneumonia and lung abscess
Wajima et al. Prevalence of macrolide resistance among group A streptococci isolated from pharyngotonsillitis
Leitner et al. Prevalence of emm types and antimicrobial susceptibility of Streptococcus dysgalactiae subsp. equisimilis in Austria
Accorsi et al. Determinants of Staphylococcus aureus carriage in the developing infant nasal microbiome
WO2023279093A1 (fr) Compositions et méthodes permettant de favoriser la santé respiratoire
Häder et al. Respiratory infections in the aging lung: implications for diagnosis, therapy, and prevention
Zhu et al. Functional insights into the high-molecular-mass penicillin-binding proteins of Streptococcus agalactiae revealed by gene deletion and transposon mutagenesis analysis
Alhamami et al. Genomic profiling of Pasteurella multocida isolated from feedlot cases of bovine respiratory disease
Xu et al. Nasopharyngeal microbiome composition associated with Streptococcus pneumoniae colonization suggests a protective role of Corynebacterium in young children
Hare et al. Streptococcus pneumoniae and chronic endobronchial infections in childhood
Chi et al. Acute otitis media caused by Streptococcus pneumoniae serotype 19A ST320 clone: epidemiological and clinical characteristics
Okamoto et al. Nasal diphtheria (chronic carriage) caused by nontoxigenic Corynebacterium diphtheriae

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 22834441

Country of ref document: EP

Kind code of ref document: A1

NENP Non-entry into the national phase

Ref country code: DE